I edited a file in Premiere Elements, inserting 15 frames of black at stratgegic points, and exported as Quicktime. I then ran the resulting file through a professional transcoder to convert to an MPEG-2 transport stream. When played back on an MPEG player (i.e., VLC) the .5 sec of black is where it's supposed to be, but if I reimport it back into Premiere Elements the black frames are mostly removed (2 out of 15 remain at each point). Why does it do this and how to prevent it? (I imported the MPEG back into Premiere to verify that there was no drift in the timeline caused by the export and transcoding process, since the black frames need to be synchronized with an ad inserter, but Premiere is removing the black frames.)
Did you Import the MPEG-2 Video? If so, it's most likely a GOP thing, when PrE internally converts to I-frame for editing. For a bit more background on GOP, see this ARTICLE.
I hope that is all that is happening and good luck,
As a test, go back to the original Project. Export/Share as DV-AVI and then Import THAT file into a New Project. Are the black frames still there, and where you left them?