I've had weirdnesses like this with Premere before. I'd guess two possibilities:

1. If there are settings within WM encoder that tell it what kind of camera it's talking to, then the settings file may have gotten corrupted. With the older versions of Premiere, you had to tell it what camcorder it was controlling, but with the newer versions, it is autosensing. Not sure about WM.

2. For an unknown reason, Premiere will just randomly decide not to talk to the camcorder and say that it isn't capable of being controlled. When this happens, I usually reboot a couple of times, in various combinations of camera off or disconnected and on and connected at time of boot. With no consistency I've been able to determine, this eventually fixes the problem.

3. If that still doesn't work, I've had success unseating and reseating the firewire card. Of course, if it's built into your motherboard, that probably won't work.

Hope that helps.