I am having the same issue as the OP, no response to IR from my brand new (from Amazon) Flirc USB 2nd gen. I have a Gen1 that I have been using for years, so I tried uploading an old config to the Gen2 and it seemed to work, but then became unresponsive after a couple of minutes. Now it seems to be completely dead. I forced a firmware upgrade via "Advanced" in the GUI and it downgraded the fw, still doesn't work.
Here are the results of flirc_util.exe, first without the flirc connected to the PC, then with. Thank you for any help you can provide!
C:\Program Files (x86)\Flirc>flirc_util.exe
Version: flirc_util.release.v3.27.16
FW Version: v4.10.5
SKU: Flirc 2.0 [dori]
Branch: release
Config: release
Hash: 0xF7261C8C
C:\Program Files (x86)\Flirc>flirc_util.exe
Version: flirc_util.release.v3.27.16
[E] lib/libtransport/transport.c _dev_send_cmd(225): Wrong response: 'dmesg_pkv' != 'versionx'
[E] lib/libtransport/hid.c hid_recv_packet(223): Wrong report exp: 5 != 1
[E] lib/libtransport/hid.c hid_recv_packet(224): hidapi: Success
[E] lib/libtransport/transport.c _recv_packet(127): _recv_packet: recv packet error = -1
[E] lib/libtransport/transport.c _dev_send_cmd(202): recv timeout
[E] lib/libtransport/hid.c hid_recv_packet(223): Wrong report exp: 1 != 5
[E] lib/libtransport/hid.c hid_recv_packet(224): hidapi: Success
[E] lib/libtransport/transport.c _recv_packet(127): _recv_packet: recv packet error = -1
[E] lib/libtransport/transport.c _dev_send_cmd(202): recv timeout
FW Version: v4.10.5
[E] lib/libtransport/hid.c hid_recv_packet(223): Wrong report exp: 1 != 5
[E] lib/libtransport/hid.c hid_recv_packet(224): hidapi: Success
[E] lib/libtransport/transport.c _recv_packet(127): _recv_packet: recv packet error = -1
[E] lib/libtransport/transport.c _dev_send_cmd(202): recv timeout
[E] lib/libflirc/firmware/fw_4.0.c fl_ver4_header_peek(50): invalid address you idiot
not a valid image
[E] lib/libtransport/hid.c hid_recv_packet(223): Wrong report exp: 5 != 1
[E] lib/libtransport/hid.c hid_recv_packet(224): hidapi: Success
[E] lib/libtransport/transport.c _recv_packet(127): _recv_packet: recv packet error = -1
[E] lib/libtransport/transport.c _dev_send_cmd(202): recv timeout
[E] lib/libtransport/hid.c hid_recv_packet(223): Wrong report exp: 1 != 5
[E] lib/libtransport/hid.c hid_recv_packet(224): hidapi: Success
[E] lib/libtransport/transport.c _recv_packet(127): _recv_packet: recv packet error = -1
[E] lib/libtransport/transport.c _dev_send_cmd(202): recv timeout
Hash: 0xF7261C8C