It is not recommended to run multiple instances of MμCalc in the same directory, as it stores all its information in the current folder and conflicts may cause unexpected behaviour. There should be no problem running separate instances in different directories.
Leaving the 3D display open can slow down calculations by a factor of two! Closing it seems to speed them back up to normal.
If the program crashes, the standard command prompt solution of pressing ctrl-c should allow you to exit under most circumstances.