The only thing I can think of that may cause the analyser to lock at startup is that the RSP PPM trim setting was set to a non-zero value. This is a known bug. You can delete the CurrentSettings.ini and Default.ini files and then try re-starting the analyser. This will cause new files to be generated that include the PPM offset being zero.
In the meantime, an updated version of the analyser is ready for release as soon as I can get the user manual updates finished. The various bug fixes in the upcoming release may stop your problem. The tracking generator system has been completely re-done and now works.