Stimulus monitor goes off, and restarting of Series 3 kernel does not help.
Delete active config file (currently Configdl.vsg) in VSG comp c:\s3kernel\SERIES3. The file is backuped in Configdl.vsg.sav, make a copy of it and rename it to Configdl.vsg.

When playing with sliders in VSGsearch.dll (PI2 control window in BrainWare), stimulus parameters get confused.
Restart system in CCC, then start script over.

While upgrading s3kernel via CCC, error occurs.
See UpgradingSeries3.html

Problem with system trigger.
Check (using scope) that trigger on BreakOut box BNC In1 looks ok (i.e. "high" state reaches 4-5 Volts).
If it is not, likely the problem is in PI2 SmartPort - VSG BreakOut box auxiliary input connection. Try to unplug it and plug again.