flac at the command line interface will be your lowest common denominator. Any GUI Software app will probably use this tool to convert anyways, sort of like foobar2000 needing to point to flac.exe. It is the official tool from the Flac developers.
The error can mean a number of things:
Most likely, a filename with extension was not properly entered: e.g. flac -d music instead of flac -d music.flac
Low disk space
Tags are incorrect: metaflac --remove -all might help to remove your tags, then flac -d
WARNING: If you do this, remember to temporarily copy your flac files as this will erase all tags.
Sometimes, you may have to repeat the process a few times.
You can also install foobar2000 over the WINE emulator in Linux to do your conversion. The playback is iffy, but conversion is fine.
I see you found something that works for you, XCFA? Excellent.
Let us know if you run into anymore hdtracks conversion problems.
Edited by Tera-Fi - 8/14/12 at 3:51am