I just pushed out an important bugfix release for Convert to FLAC. When testing the new multiple input file support, I apparently never bothered testing it on files with spaces in their names. Oops. Version 2.0.1 fixes this oversight.
Relevant links below. If you've already upgraded to v2.0, please download this new version ASAP. Sorry for the inconvenience.
For more information:
Convert to FLAC home page and downloads
Convert to FLAC ChangeLog