Seems like a "convert to DNG" and "rename" allows LR to reimport duplicates even though "Don't import suspected duplicates" is checked. Shouldn't the database keep track of original filenames/types?
Lr keeps track of original filenames, but only "as imported". In other words, "before renaming in Lightroom" (NOT "before renaming for import"). And such might be OK if it compared incoming filename after conversion to DNG but from what you're saying, it sound like it doesn't.