After chasing the threads with the tap, make sure to try to run the new screw in sans the base, and torque to the selected value before attempting to re-install the base.
If the holes in the scope base are misaligned in any way- this would prevent the screw from threading in freely and possibly result in what you're seeing, there's very small clearances here.
Same thing could happen if the hole in the receiver were misaligned, but that's less likely. Only takes a few thousandths to be a problem.
In any case, if the screw threads in properly after re-tapping- and you run into any resistance threading in when installing the base, STOP and take it to a smith. Either the hole in the base, or the receiver is misaligned.