Did you make sure all your subtools are named differently? Zbrush will NOT pre-process all if any 2 subtools are named the same. You have to be sure that every subtool has a unique name.
@iconplast, I have Uniform Mesh, 6 Threads, Delete Caches at Start and 64 Bits Decimator selected. I mainly messed around with the Threads and 64/32 bit settings. @couto, I tried it both running in the background and always keeping it up. I left it up without clicking on anything for about 15-20 minutes once and still…