Rear end "clunk"

06 Toyota highlander “clunks” when backing up. Always in the morning (when not driven for a while) and usually loud for the first 4 or 5 rotations. Then you can barely hear it. Put it up on a hoist and wheel won’t do a full rotation before it seizes up and you have to really struggle to get it to move. I want to say you can VERY faintly hear the “clunk” in forward also but when on the hoist seems to turn freely. Replaced gear lube in rear differential. No metal shavings. Any suggestions? Thanks

U-joints on the driveshaft - some are serviceable some are not - then you just have to replace it. Get under it and see if you can twist the shaft in either direction ( slack )

Which one, seizes or turns freely while on hoist? or turns freely forward and seizes reverse?
Does this Highlander have a locking differential?

When on the hoist, the drivers side rear will turn freely, all day. If you take the same wheel and turn it backwards, it will make almost a full rotation and seize up. I can get it to make a full rotation, backwards, but it takes a bit of a struggle. There is a push button 4 wheel drive in the highlander. It has new calipers, roater and pads on both rear wheels. As far as locking differential, I don’t think so. Nothing you physically have to get out and lock into 4 wheel. The wheel bearings were also replaced all the way around the vehicle about 2 years ago. With that said, I don’t remember if the dealership replaces all the wheel bearings or all the wheel hub bearings. It’s my understanding the are 2 sets on each wheel? Thanks

Try the same rear wheel experiments after disconnecting the drive shaft between the xfer case and the rear differential. Should help narrow it down. Before removing the driveshaft, scribe some witness marks on the driveshaft and what it bolts to on each end, so you can re-install it with the same orientation. I’m guessing you have a problem of some sort inside the differential.