V12 rendered clip duration shorter than timeline

Ros wrote on 4/17/2013, 6:27 PM
I have rendered a series of 3 clips that are precisely timed at 24 minutes on the timeline.
When I render them to 720 x 480 mpeg2 at 23.976 + 2-3 pulldown using MainConcept, my 24min. video is missing about 3 seconds. All 3 clips end up abruptly, while on the timeline they fade to black on 5 frames while opaque black is on for 6 more frames. So basically each clip is missing a second.

I have done this many times only now I am not getting the proper duration.
I have tried V12 build 486 and 563 with no positive results and with other videos as well.

What could possibly go wrong?