Is there something unusual about the videos? Are they things you shot…downloaded?
Compressor doesn't resize videos unless instructed to. I would re-check the size of the originals by opening QuickTime and hitting command i. Verify that it is 1080. If it is and you use the 1080 Apple Device preset, it shouldn't change the size.
As far as frame rate is concerned, although I don't know a lot about iPads, I'd be surprised if it mattered in playback whether they were 50 fps or 5 fps.