Yes, Filter Forge currently has no means of customization locations for storing temporary files (not unlike Photoshop scratch file) on disks other than system (in fact, we use the system-configured temporary folders for that).
We're considering adding ability to specify the temporary location (filters and settings are stored in your profile, but they take only several megabytes of disk space, so this isn't a problem).
Unfortunately, the bug you encounter has nothing to do with free disk space -- it's a major resource leak that we're exploiting right now. Looks like it occurs after a long sessions with Filter Forge, but we currently don't know exact reasons.
Nevertheless, we'll fix it sooner or later