That is odd behavior indeed. As the Motion Effect is a fixed Effect, I would guess that when the Project is created, the necessary XML is written for it, at that time. Where it goes, is anybody's guess. I've not read of this happening before, but maybe there is a Bug in a new upgrade.
Good luck, and I'll follow this thread with interest.
There was a really old post here:
and a more recent here with a couple of posters reporting the problem:
The work-around of saving a preset and re-applying it to the affected clips saved my project luckily!
Trouble is, reporting this bug is difficult as I don't know at what stage the problem occured - I have seen this behaviour a couple of times though in un-related projects over the past few months.
Thanks for those discussion links. I either missed those, or have just forgotten.
It seemed that in both cases, there were version differences, say PrPro CS3 Projects into CS4, or similar.