Driveshaft too short after 3" lowering blocks

Maybe the 93 & 91 axles are not identical... Maybe the distance from the axle-center-line to the shaft mounting flange are not the same...

Ive never heard of anyone having any problems

This is just exactly it, I have not had problems and have been doing this for 20+ years.

I would put the driveshaft in and then do the blocks, put one side of the axle on and put the U-bolts in loose, then put the other side on.

This may be the problem, when you out the blocks in and then try to put the driveshaft in, it can cause a problem.