I just started using subroutines for cutting some slots in material. Nothing fancy. The first piece cut perfectly. When I ran it a second time, it was running fine through the first 21 slots, but for the 22nd slot, there was a clamp in the way. I PAUSED Mach3 and move the clamp. When I went to resume, the subroutine threw an error, returned, then started cutting another slot, but the offset calculation within the subroutines got messed up.

Anyone ever had problems with PAUSE causing weirdness either in normal G-Code or in subroutines?

Yes I have had problems with pausing in subroutines. I don't use them anymore so I haven’t had any problems pausing the program.