Hmm... you know, I think I actually ran into this with a client, and the recourse at the time was to simply disable account validation. I tend to think it should work without having to resort to that, but I'd honestly recommend it for conversion purposes anyways (unless you just really really need account moderation). Also, it may be a bug that got massaged out in the actual 1.3 release (the one after RC1).

Thanks for your kind words.

EDIT: Looking at the source, the offending function is uc_cart_user() in uc_cart.module. I do believe you're right about the session rebuilding... if the user was to login at the time they created the account, the cart should be updated no problem. Honestly, I think a good solution moving forward would be to not use the session ID but actually have a cart ID session variable. Seems like a no brainer.