Not sure if this helps with troubleshooting, but I threw the flirc into an ubuntu VM, installed the application [v1.2.6] and attempted a force upgrade.
There's an I/O error in the console output right after the firmware update, I assume this is part of the issue.
Note: Running as root
root@ubuntu:~# Flirc fl_open_devices(344): trying to open: 20A0 :: flirc.tv
[D] fl_open_devices(390):
1d6b:0002 (bus 1, device 1)
[D] fl_open_devices(390):
20a0:0001 (bus 2, device 7)
[D] fl_open_devices(433): Vendor: flirc.tv
[D] fl_open_devices(453): [Vendor Match]
fl_open_devices(461): usb port:2
[D] fl_open_devices(390):
0e0f:0008 (bus 2, device 4)
[D] fl_open_devices(390):
0e0f:0002 (bus 2, device 3)
[D] fl_open_devices(390):
0e0f:0003 (bus 2, device 2)
[D] fl_open_devices(390):
1d6b:0001 (bus 2, device 1)
[D] fl_open_device(135): Firmware v:2.6
[D] determine_iface(46): fw_state: firmware
[D] determine_iface(47): version: 2.6
[D] determine_iface(99): initializing fw ver2.6 CheckFirmwareVersion(402): hw version: 2.6
CheckFirmwareVersion(403): emb version: 2.600000
[D] checkHardwareStatus(170): state: normal
[D] checkHardwareStatus(170): state: normal
[D] checkHardwareStatus(170): state: normal
[D] checkHardwareStatus(170): state: normal
[V] fw_upg_clicked(144): force fw upgrade clicked
[V] force_update(338): force update slot
[D] checkHardwareStatus(170): state: normal
[D] checkHardwareStatus(170): state: normal
[D] checkHardwareStatus(170): state: normal
[D] checkHardwareStatus(170): state: normal
[D] checkHardwareStatus(170): state: normal
[D] do_embedded_upgrade(376): trying upgrade[D] fl_send_msg(164): Input/output error
[D] do_embedded_upgrade(379): device was not in bootloader, closing
fl_close_device(330): closing device handle
[DEVICE] Waiting fl_open_devices(344): trying to open: 20A0 :: flirc.tv
[D] fl_open_devices(390):
1d6b:0002 (bus 1, device 1)
[D] fl_open_devices(390):
20a0:0001 (bus 2, device 7)
[E] fl_open_devices(428): Cannot query device, is the GUI open?
[D] fl_open_devices(390):
0e0f:0008 (bus 2, device 4)
[D] fl_open_devices(390):
0e0f:0002 (bus 2, device 3)
[D] fl_open_devices(390):
0e0f:0003 (bus 2, device 2)
[D] fl_open_devices(390):
1d6b:0001 (bus 2, device 1)
fl_open_devices(344): trying to open: 20A0 :: claylogic.com
[D] fl_open_devices(390):
1d6b:0002 (bus 1, device 1)
[D] fl_open_devices(390):
20a0:0001 (bus 2, device 7)
[D] fl_open_devices(390):
0e0f:0008 (bus 2, device 4)
[D] fl_open_devices(390):
0e0f:0002 (bus 2, device 3)
[D] fl_open_devices(390):
0e0f:0003 (bus 2, device 2)
[D] fl_open_devices(390):
1d6b:0001 (bus 2, device 1)
[D] _fl_open_device(491):
No devices found
[D] fl_open_device(123): no device found
. fl_open_devices(344): trying to open: 20A0 :: flirc.tv
[D] fl_open_devices(390):
1d6b:0002 (bus 1, device 1)
[D] fl_open_devices(390):
20a0:0001 (bus 2, device 7)
[E] fl_open_devices(428): Cannot query device, is the GUI open?
[D] fl_open_devices(390):
0e0f:0008 (bus 2, device 4)
[D] fl_open_devices(390):
0e0f:0002 (bus 2, device 3)
[D] fl_open_devices(390):
0e0f:0003 (bus 2, device 2)
[D] fl_open_devices(390):
1d6b:0001 (bus 2, device 1)
fl_open_devices(344): trying to open: 20A0 :: claylogic.com
[D] fl_open_devices(390):
1d6b:0002 (bus 1, device 1)
[D] fl_open_devices(390):
20a0:0001 (bus 2, device 7)
[D] fl_open_devices(390):
0e0f:0008 (bus 2, device 4)
[D] fl_open_devices(390):
0e0f:0002 (bus 2, device 3)
[D] fl_open_devices(390):
0e0f:0003 (bus 2, device 2)
[D] fl_open_devices(390):
1d6b:0001 (bus 2, device 1)
[D] _fl_open_device(491):
No devices found
[D] fl_open_device(123): no device found
. fl_open_devices(344): trying to open: 20A0 :: flirc.tv
[D] fl_open_devices(390):
20a0:0000 (bus 2, device 8)
[D] fl_open_devices(390):
1d6b:0002 (bus 1, device 1)
[D] fl_open_devices(390):
0e0f:0008 (bus 2, device 4)
[D] fl_open_devices(390):
0e0f:0002 (bus 2, device 3)
[D] fl_open_devices(390):
0e0f:0003 (bus 2, device 2)
[D] fl_open_devices(390):
1d6b:0001 (bus 2, device 1)
fl_open_devices(344): trying to open: 20A0 :: claylogic.com
[D] fl_open_devices(390):
20a0:0000 (bus 2, device 8)
fl_open_devices(407): claiming interface 0
[D] fl_open_devices(433): Vendor: claylogic.com
[D] fl_open_devices(453): [Vendor Match]
fl_open_devices(461): usb port:2
[D] fl_open_devices(474): bootloader found
[D] fl_open_devices(390):
1d6b:0002 (bus 1, device 1)
[D] fl_open_devices(390):
0e0f:0008 (bus 2, device 4)
[D] fl_open_devices(390):
0e0f:0002 (bus 2, device 3)
[D] fl_open_devices(390):
0e0f:0003 (bus 2, device 2)
[D] fl_open_devices(390):
1d6b:0001 (bus 2, device 1)
[D] fl_open_device(133): Bootloader v:1.4
[D] determine_iface(46): fw_state: bootloader
[D] determine_iface(47): version: 1.4
[D] determine_iface(51): initializing btldr ver1
[DEVICE] Bootloader Detected
[D] do_embedded_upgrade(387): using legacy image
fl_upgrade_fw_ext(899): bootloader open
[DEVICE] Uploading
[D] fl_ver1_get_dev_info(109): size of data returned: 7
[D] fl_ver1_get_dev_info(110): page size: 128
[D] fl_ver1_get_dev_info(111): device size: 32767
fl_ver1_pre_boot(197): settings: B3
[========================================>] 100%
[D] fl_send_msg(164): Input/output error
fl_close_device(330): closing device handle
[DEVICE] Waiting fl_open_devices(344): trying to open: 20A0 :: flirc.tv
[D] fl_open_devices(390):
20a0:0000 (bus 2, device 8)
[D] fl_open_devices(390):
1d6b:0002 (bus 1, device 1)
[D] fl_open_devices(390):
0e0f:0008 (bus 2, device 4)
[D] fl_open_devices(390):
0e0f:0002 (bus 2, device 3)
[D] fl_open_devices(390):
0e0f:0003 (bus 2, device 2)
[D] fl_open_devices(390):
1d6b:0001 (bus 2, device 1)
fl_open_devices(344): trying to open: 20A0 :: claylogic.com
[D] fl_open_devices(390):
20a0:0000 (bus 2, device 8)
fl_open_devices(407): claiming interface 0
[E] fl_open_devices(428): Cannot query device, is the GUI open?
[D] fl_open_devices(390):
1d6b:0002 (bus 1, device 1)
[D] fl_open_devices(390):
0e0f:0008 (bus 2, device 4)
[D] fl_open_devices(390):
0e0f:0002 (bus 2, device 3)
[D] fl_open_devices(390):
0e0f:0003 (bus 2, device 2)
[D] fl_open_devices(390):
1d6b:0001 (bus 2, device 1)
[D] _fl_open_device(491):
No devices found
[D] fl_open_device(123): no device found
. fl_open_devices(344): trying to open: 20A0 :: flirc.tv
[D] fl_open_devices(390):
1d6b:0002 (bus 1, device 1)
[D] fl_open_devices(390):
0e0f:0008 (bus 2, device 4)
[D] fl_open_devices(390):
0e0f:0002 (bus 2, device 3)
[D] fl_open_devices(390):
0e0f:0003 (bus 2, device 2)
[D] fl_open_devices(390):
1d6b:0001 (bus 2, device 1)
fl_open_devices(344): trying to open: 20A0 :: claylogic.com
[D] fl_open_devices(390):
1d6b:0002 (bus 1, device 1)
[D] fl_open_devices(390):
0e0f:0008 (bus 2, device 4)
[D] fl_open_devices(390):
0e0f:0002 (bus 2, device 3)
[D] fl_open_devices(390):
0e0f:0003 (bus 2, device 2)
[D] fl_open_devices(390):
1d6b:0001 (bus 2, device 1)
[D] _fl_open_device(491):
No devices found
[D] fl_open_device(123): no device found
. fl_open_devices(344): trying to open: 20A0 :: flirc.tv
[D] fl_open_devices(390):
20a0:0001 (bus 2, device 9)
[E] fl_open_devices(428): Cannot query device, is the GUI open?
[D] fl_open_devices(390):
1d6b:0002 (bus 1, device 1)
[D] fl_open_devices(390):
0e0f:0008 (bus 2, device 4)
[D] fl_open_devices(390):
0e0f:0002 (bus 2, device 3)
[D] fl_open_devices(390):
0e0f:0003 (bus 2, device 2)
[D] fl_open_devices(390):
1d6b:0001 (bus 2, device 1)
fl_open_devices(344): trying to open: 20A0 :: claylogic.com
[D] fl_open_devices(390):
20a0:0001 (bus 2, device 9)
[D] fl_open_devices(390):
1d6b:0002 (bus 1, device 1)
[D] fl_open_devices(390):
0e0f:0008 (bus 2, device 4)
[D] fl_open_devices(390):
0e0f:0002 (bus 2, device 3)
[D] fl_open_devices(390):
0e0f:0003 (bus 2, device 2)
[D] fl_open_devices(390):
1d6b:0001 (bus 2, device 1)
[D] _fl_open_device(491):
No devices found
[D] fl_open_device(123): no device found
. fl_open_devices(344): trying to open: 20A0 :: flirc.tv
[D] fl_open_devices(390):
20a0:0001 (bus 2, device 9)
[D] fl_open_devices(433): Vendor: flirc.tv
[D] fl_open_devices(453): [Vendor Match]
fl_open_devices(461): usb port:2
[D] fl_open_devices(390):
1d6b:0002 (bus 1, device 1)
[D] fl_open_devices(390):
0e0f:0008 (bus 2, device 4)
[D] fl_open_devices(390):
0e0f:0002 (bus 2, device 3)
[D] fl_open_devices(390):
0e0f:0003 (bus 2, device 2)
[D] fl_open_devices(390):
1d6b:0001 (bus 2, device 1)
[D] fl_open_device(135): Firmware v:2.6
[D] determine_iface(46): fw_state: firmware
[D] determine_iface(47): version: 2.6
[D] determine_iface(99): initializing fw ver2.6
[DEVICE] FW Detected
[DEVICE] EOK
do_embedded_upgrade(393): done with upgrade
[D] checkHardwareStatus(170): state: normal
[D] checkHardwareStatus(170): state: normal <closed application>
root@ubuntu:~# flirc_util status
Last upgrade attempt: Error
root@ubuntu:~# flirc_util version
flirc_util version v1.2.6 [v1.2.6]
Firmware: v2.6