I'm actually suddenely having sync problems with multiple iPods as well. Every time I switch to the "other" iPod, it forgets the first one, and asks me if I want to use it as a handheld player. It's interesting to note, however, that MC still remembers all the settings for this iPod -- i.e. when I say "yes," it comes up with the handheld config screen, and the settings are correct. Even the specific playlist I use for this iPod is correctly checked.
One of the iPods connects to the system via USB2 (a 5G) while the other one connects via firewire (3G.) I'm not trying to sync them while both are connected -- I eject one and connect the other.
On a side note, the MC "eject" feature is no longer working. I have to use the windows taskbar "eject" feature to eject the iPod.
There have been several changes to the iPod recently (since around 188 or 190), so I believe that one of these may have messed up the iPod functionality a bit. I didn't have these issues a month or so ago.
Thanks,
Larry