Motion Transition Glitch - DVDSP 3

I'm relatively new to DVDSP, but I've successfully used the Menu Transition feature on a number of occations. I find it much easier and much faster than building my own transitions, especially when dealing with large numbers of menus. This is the first time that I've run into trouble.
I recently authored a project with 7 menus. 6 of the menus were "motion" menus comprised of a .pct bacground file and a .pct overlay file with an .AC3 audio track. These 6 menus were set to loop after the audio track finished playing. The 7th menu was a true motion menu with an .m2v background and a .pct overlay and again with an .AC3 audio track. This menu was set to pause on a still at the end of it's run.
I built and formated the project without incident and it played back correctly on all test systems (MAC, PC, Set-top). After reviewing the check disk the client requested that menu trasitions be added. I added the transitions and built and formated the project (after checking the disk in the simulator) reusing the original build folder. Upon review of the disk, I was shocked and confused when I discovered that rather than the motion dissolve transition that I expected to see inbetween menus, I was instead seeing seemingly random sections of my 7th motion video menu. I attempted to delete the build folder and and rebuild the disk from scratch, but to no avail. Same problem.
I was successful in solving the problem by doing three things (I'm not sure which was responsible for fixing the glitch) by saving the project under a different name (and building it in a different build folder), by removing and reapplying all of the transitions, and by removing and replacing (with the same files) the .m2v and .AC3 files from my motion menu.
Now that I've solved my own problem (during the course of writing this post), I guess that my question has become: Has anyone else encountered this particular glitch and is there a way for me to avoid it in the future?

I've tried to follow the steps in the Building an Alpha Transition, but it says that you need 2-3 different files, but no mention on exactly how to make those.
I exported from motion and have a file named Trans1-Animation NTSC Alpha.mov but I think I still need to create other files. All the tutorials that I can find show how to do this in After Effects but none explain how to create the need files from motion.
Is there a tutorial that explains the process in motion?
Powermac G5, Final Cut Studio Mac OS X (10.4.6)

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