driveline sounds when using the spare tire

[Flyer1]

A couple months ago I got a flat on the right rear tire of my '04 X3 (3.0, 6-speed manual) so I had to use the space saver spare for the first time. Driving on the spare, it created what I'll describe as a bindng in the driveline. When starting off, and especially when turning, its as if there is tension that builds up and then a clunk as it pops free. It occurs in 1st gear when starting out. My guess is its in the transfer case. It is as if the spare is the wrong size and it created a speed mismatch between the front and back wheels that the x-fer case can't handle. You could hear and feel it. When accelerating from a stop, its like someone applied the brakes for a microsecond. The acceration wasn't smooth. It basically happens once, maybe twice when starting from a stop. I don't really notice it while cruising around.

I drove on the space for a month while I chased around to get new tires. I have since gotten new rear tires and the problem is mostly gone, but every so often I can feel it, but its not nearly as bad, or as often.

Anyone else experienced this? My spare is the correct size and was properly inflated. I'm wondering if its an indication of a problem with the driveline. The car just turned 99k miles.

Thanks
Chip