Can you please upload a screenshot with View Hidden Characters turned on of the page before the jump and after the jump (2 screenshots)?
This is the jump. One key point I failed to mention (or am not sure if I made clear enough) is that in InDesign it is correct. But in the PDF output it adds the indent on its own.
Yes, that is certainly key! Those bugs are quite serious and really should not happen. Are you running the current version? 7.0.4 for CS5, 6.0.6 for CS4 or 7.5.1 for CS5.5? I believe a bunch of those were fixed by 7.0.4...