The software change needs to be in the FLAC liibrary that is used by Firefly. I have no issues running Firefly on my NSLU2, only under Windows on PC. The difference is the audio library that is used. I think NSLU2 uses libflac, whereas the PC version of Firefly uses ffmpeg (I think) and I understand that it is ffmpeg that needs updating for the Windows version to work.
This is not a Roku or iTunes issue since neither knows anything about FLAC – Firelfy transcodes FLAC to WAV. The reason that you see the error is simply that Firefly is able to report that there is an error from the transcoding function.