Jason, after reading your email I decided to use a third machine running Windows 8.1 x64 and a fresh install of Flirc to try the upgrade from a different USB chipset.
I was unable to upgrade the Flirc initially, but after uninstalling and reinstalling the Flirc software a second time (and deleting drivers) I was able to upgrade the firmware... I didn't change anything between the first and second attempt so I'm not sure why it worked the second time. I was able to fix the second non-working Flirc the same way. The same procedure didn't work on the first two machiens.
Furthermore as the USB drivers on the first two machines were fully up to date I can only assume the Flirc and their USB chipsets/drivers just don't get on together when updating firmware...?!