Pathologic filter doesn't work with all text formats

Pathologic filter doesn't work with all text formats. It works just fine with my "Full HTML" text format (unfiltered), but it does nothing for my "HTML" text format (filtered). I have the exact same configuration for both text formats regarding Pathologic. That is, the "Correct URLs with Pathologic" checkbox is checked and the "Correct URLs with Pathologic" filter is at the bottom (last) position in the filter list, per the recommendation. I have not yet tried turning my "HTML" text format into an unfiltered format to troubleshoot; I'm reluctant to do so because then it would be useless to me, as it needs to be filtered. What gives? Please help.