Hi Ed,
I can confirm your observation!
A nuisance of thing.
I have a 53 second scene, where I want 3 images sharing the video screen simultaneously.
As I want the three clips to change priority during the scene for two times, I have to re-arrange them among VT1, VT2 and VT3.
And to be able to produce transitions between the different priority clips, I repeat the 53 seconds for 3 times in total, parted with a (approx.) 2 second pause between them, respectively.
For graphic explanation:
VT1 contains: CLIP_A <pause> CLIP_B <pause> CLIP_B
VT2 contains: CLIP_B <pause> CLIP_A <pause> CLIP_C
VT3 contains: CLIP_C <pause> CLIP_C <pause> CLIP_A
In the final video I take the first part of the first repetition, the middle part of the second repetition, and the finale of the third repetition, setting the transition of desire between them.
But when pre-rendering this interimistic project into a MPG4 file format I encountered the problem, that CLIP_A in the second block (in VT2) hangs as you describe.
It took me 2 or 3 attempts of rendering to get the thing work.
No consistenty in this problem, seems arbitrary.
Michael.