1999 chevrolet silverado 1500 when i start it up it makes a clunk under the truck, it sounds like it comes near the transfer case or transmission. Also it is 4x4 and it is an automatic. Does anyone know what this could be?

the transfer case only engages when in 4wd. check the universal joint, it connects from the drive shaft to the rear differential. it may need grease or to be replaced.

I would check for a bad wheel bearing on the rear, also check the u-joints on the drive shaft.

never knew 4x4 had a chain inside the box ??

The transfer case is behind the transmission your drive shafts attach to it look for some wires coming out of it that should be the actuator. Hope this helps.

It could be a bad U-Joint on the drive shaft.

It could vary well be U-joints or maybe a broken mount, loose bolts. I've the bolts come loose that hold the transfer case to the transmission they will usually leak fluid when that happens.

its hard to believe 2 trucks with same noise. you really need to verify where noise is from. it could be the trans

It sounds like your 4WD is still engaged and you need to have it serviced. It's common for the 4wd to get stuck in the on position with the button pushed to the 2wd mode. As you turn the front wheels are binding with the rear wheels. There is a vacuum switch on top if the transfer case on the drivers side that may have gone bad and needs to be replaced. You can pick it up at Auto Zone for $25.00 and $85.00 at the dealer, there is three vacuum hose attached to it that needs to be disconnected and then the switch can be un screwed from the transfer case like a spark plug.. Good luck and hope this helps. keep me posted, be glad to answer any question you may have. 

The noise is caused by the axle button being worn out, this lets the axle move back and forth and clunk, this is a unique problem with C clip retained axles, it is a noise issue but will not fail and cause any more damage, in order to fix it you must have the axles pulled and the diff carrier checked for excess wear where the axle retainning C clip rides, if the carrier is ok then replace the axles.

try checking all fuses the ones in the fuse box inside as well as under the hood. sometimes you have to check the fuses because of a wire touching in the transmission before you had it rebuilt. Try that out and if not I would go back to whom ever rebuilt the transmission.. I have turning wrenches for 22 years and the last ten in my own shop. I come across allot of 99 silverados with trans and transfer case problems. Hope you find a burnt fuse.