Wrong frame-rate, corrupted playback of isom/mp4 files remuxed from H.264/AC3 MPEG-TS
To answer part of your question (and add a couple of other abbreviations you will run into):


PTS = Presentation Time Stamp
DTS = Decode Time Stamp
PCR = Program Clock Reference
SCR = System Clock Reference


MPEG elementary streams reorder the frames for transmission. The PTS indicates the order that the frames should be re-assembled into. The DTS lets the decoder know if a frame needs to be decoded earlier than it is displayed (because a P or B frame references it). The PCR or SCR are the time scale that the PTS and DTS reference.

tstools and other transport stream analyzers can help you determine if the PCR/PTS/DTS issue is in the source file or not.