I just pushed out an updated Convert to FLAC release to fix a bug involving spaces in filenames. Again. In my defense, though, the root cause is completely different this time, and was limited to only APE or TTA input files (it was due to an odd way I had to deal with output redirection on some of the conversion commands). I've renamed my test files to include spaces, so hopefully this shouldn't happen again. Twice is definitely enough.
For more information:
Convert to FLAC home page and downloads
Convert to FLAC ChangeLog