Are you browsing away from zbrush while this happens? The way ZBrush works is with scripts, and it must always be the main program on your screen in order for it to work properly. When it's pre-processing, just leave your computer alone and go watch some TV. Minimizing/switching windows will stop it.
I think I have this same issue. :( So, freshly launched ZBrush, spawned a
Cylinder3D. Make Polymesh3D. Pre-process Current and this prints in the upper
left after flashing “Computing please wait…” and hitches forever, seemingly. I
can Esc out to “ZScript Aborted”.