More than 2 images delay processing into infinity


I’ve been having this problem with Cell Profiler which renders me unable to process more than 2 image sets at the same time regardless of which pipeline I use. Now this a big problem for us as we would like to use the software to analyze morphology of fibroblasts based on images taken from a 96 well plate. If I analyze 2 image sets the software finishes without problems after less than 10 minutes. Anything more than that leads to the mentioned problems.
I know that most people here have used the software longer than I do and so I wanted to know if there is a special trick to resolve this. Thanks in advance!

My system: Windows 7 64 bit, 16 GB DDR3 RAM, i7 2600k at base settings and some Radeon graphics card