do you have HID's "boot protocol" implemented? Do not have flirc device here to check HID "Sub Class" and "Protocol" parameters.
from wiki (http://en.wikipedia.org/wiki/Human_interface_device)
"... HID also defines "boot protocol". In boot protocol, only specific devices are supported with only specific features because fixed data packet formats are used. The HID descriptor is not used in this mode so innovation is limited. However, the benefit is that minimal functionality is still possible on hosts that otherwise would be unable to support HID. The only devices supported in boot protocol are
Keyboard — Any of the first 256 key codes ("Usages") defined in the HID Usage Tables, Usage Page 7 can be reported by a keyboard using the boot protocol, but most systems only handle a subset of these keys. Most systems support all 104 keys on the IBM AT-101layout, plus the three extra keys designed for Microsoft Windows 95. Many systems also support additional keys on basic western European 105-, Korean 106-, Brazilian ABNT 107- and Japanese DOS/V 109-key layouts. Buttons, knobs and keys that are not reported on Usage Page 7 are not available. For example, a particular US keyboard's QWERTY keys will function but the Calculator and Logoff keys will not because they are defined on Usage Page 12 and cannot be reported in boot protocol.
Mouse — Only the X-axis, Y-axis, and the first 3 buttons will be available. Any additional features on the mouse will not function.
One common usage of boot mode is during the first moments of a computer's boot up sequence. Directly configuring a computer's BIOS is often done using only boot mode. Sometimes a message will appear informing the user that the device has installed the correct driver and is now usable."
http://www.usb.org/developers/devclass_docs/HID1_11.pdf
Page 75
F.5 Keyboard: Using the Keyboard Boot Protocol
Edit:
Device descriptor of working keyboard bios mode:
bInterfaceClass 3 Human Interface Device
bInterfaceSubClass 1 Boot Interface Subclass
bInterfaceProtocol 1 Keyboard
Device descriptor of flirc non working bios mode:
bInterfaceClass 3 Human Interface Device
bInterfaceSubClass 0 No Subclass
bInterfaceProtocol 1 Keyboard