Hm. Well, it seems to be saying that the asset is newly "untranscoded" when I open up the project again. Still, burning to an .iso solves things, and (since I don't have the newer versions of Toast), I just burn copies off the .iso in Encore. Happy days!
3D isn't an issue, since this is just a side-by-side thing, not a full-on MVC dual-HD stream encoding. Good enough for now!
Thanks for the help! and the advice re: CS6. For some reason I thought 5.5 was already 64-bit. Worth the upgrade, I think.