I found a way to reproduce the problem with a simple project.
Since I suspect that the problem is related to the type of source file,
download the following two files:

http://www.KVI.nl/~zwarts/Src1.MOD
http://www.KVI.nl/~zwarts/Src2.MOD
from http://www.KVI.nl/~zwarts

Start a new project and place Src1 on the time line.
Cut this scene at 8.00 seconds. (I don't know if it needs to be exact, but why not?)
Insert Src2 in between these two scenes.
Select all three scenes, copy and paste them 100 times. (Many times, hundred sounds nice.)
Now go to Make Movie and try to create a DVD compatible MPEG2 file.
I tried it a few times and it always stopped before about 10% of the scenes.
I would like to know the results of others. How far did it go for you?