I think we all believed that the release of Tiger with its SyncServices engines would resolve most issues. Even I repeatedly said words to that effect—based upon pre-release information—but I was disappointed, to say the least.
I'm not sure why the support staff at Mark/Space indicated that you should turn off Automatic synchronization with .Mac, as I am a long time .Mac user, have .Mac Sync set to automatically synchronize, and have no problems whatsover. I don't understand how iSync and the SyncServices framework could be interferring in any way with the Missing Sync, as it uses the SyncServices framework itself to perform synchronization tasks. And if version 5 or later is installed, it deactivates the iSync Palm Conduit, so there is no way that the two applications would interact.
Going back to Mac OS X 10.3.9 would give you unified iSync or Missing Sync synchronization, but that seems like a huge step backward. SyncServices is clearly the way of the future in synchronization under Mac OS X. Even Microsoft has now just released a SyncServices-savvy version of Entourage.
What sort of error messages are you getting exactly? I never get any, a typical synchronization event is less than two minutes at maximum with my Treo 600 via USB, and I have long synchronized automatically with .Mac.
Did you do what they recommend and replace all of the data on your device the first time you synchronized by setting each Mark/Space conduit—Contacts, Events and Tasks—to Overwrite handheld with desktop data? If you did not do that, it is likely the root of your error conditions. It really is a critical first step.
I've been using 5.1.0 beta 18 for some time and have had no issues at all. I don't recommend that you install such beta software if the release version—currently 5.0.3—is not working properly for you, because it indicates that most such issues will also appear in the beta release, and you are not offered support with pre-release software. I had no issues under 5.0.3 either, except with regard to a couple of very minor problems resolved in the pre-release 5.1 packages. Most users would never even have encountered them.