This kind of thing is very likely to be a firmware thing than a PCB/hardware thing.
During BIOS/boot phase, the USB drivers used are not the usual ones in your system (be it windows or linux), but ones which are coded in BIOS/EFI (whatever your PC comes with). They are often somewhat simple/non-standard, crippled and behave strangely (e.g. do not properly advertise the boot protocol).
The problems usually arise when the firmware supports NKRO (because NKRO requires a different USB communication that the "usual" 6KRO, and the NKRO protocol is definitely not supported by BIOSes). BIOS is supposed to let the keyboard know that it should work in "boot protocol", i.e. the traditional 6KRO, but they don't always do that.
Various firmwares that are available for custom PCBs deal with these problems in various ways, and use different ways of "guessing" when they communicate with BIOS and when with a normal system.
So - I would recommend trying out different firmwares on the Red Scarf, to see if behaviour during BIOS/boot changes or not. This might be tricky, since I think only TMK supports Red Scarf at the moment. However you can try to disable NKRO and see if this "helps".
EDIT: As far as checking sniffing the USB traffic goes, you'd need a hardware USB sniffer since you need to have a look at what's happening when your PC is booting. That's expensive.