Are you trying to create a multi angle disc or a mixed angle disc - i.e are you running the alternate angle for the length of the original footage or are you ahveing only a few sections here and there as an alternative section for the viewer?
Getting these right requires you to be particularly exact in how you create your footage. For example, the two clips must be an exact GOP structure, length and so on. Keep in mind that when you put a cut in the FCP timeline and export the footage you could be adding a compression marker. If the cut in one piece doesn't match the same point in the other then the GOP structure will be different, and your build will fail.
What I suggest you do is to not use compressor for making your files but to use DVDSP and make the encode settings CBR instead of VBR. This is the *only* time I will recommend using the built in encoding function of DVDSP. CBR is in fact pretty essential to get your angles working, too.
If you still have problems (and you shouldn't) try exporting out of FCP as a single piece of footage, then import that back in to FCP so that the timeline shows a single clip, no cuts. Now export that again... then try it. You should make sure each clip is the exact same length, to the frame and then import to DVDSP.