More than anything else, this seems to be a resource issue. I've noticed on my 5455 with WM2003 that if I don't have at least 13MB of Free RAM on the Storage side, that I'm going to run into problems.
I never have more than 2-3 apps running at a time, so I always have at least 13MB of free RAM on the Program side. But then again, I had my 5455 upgraded to 128MB of RAM by PPC Techs, so I have storage to spare...
There's not much that you're going to be able to do about this. The things I have noticed that help are often done after a Hard Reset. If Wi-Fi is the first thing you set up (or one of the first things) after a Hard Reset, then my 5400 seems to "remember" everything its supposed to, and synching works with either BT or Wi-Fi. You're going to have to play around with it.
However, I truly believe this to be a resource issue on the 5400. The best thing to do, IMHO, is to get the memory upgrade from PPC Techs (if you can afford it), and then guard your native RAM. Don't install anything to it that doesn't HAVE to be installed there (apps like Pocket Informant, Today Plug-Ins, and Snoopsoft Dashboard HAVE to be installed to native RAM to work right...)
Upgrading to AS 3.7.1 will help out a great deal, but unfortunately, there's no universal cure. I wish there was.
Kind Regards,
Christopher Spera