J,
I've experienced this in a very bad way and have reported it to Mark as
a bug. In some cases, even if you try to reformat a section (e.g.,
change font size), it reverts back to the font it was in the pdf. The
only workaround I've found to that is to re-type the text in by hand.
That's unfortunate.
The Remove Font Style button (eraser, Ctrl+\) should be the work-around for that problem. If even it won't clear out the pasted formatting that's a problem.
I don't know if you tried it, but it may also be possible to clear out the pasted formatting by using Code View (the "</>" button), but that oughtn't be necessary - it requires some knowledge of HTML coding probably more than a little patience.
Shal