Do you see an improvement if you move Freeze Window up so that it is the very first step in this script?
Show All Records in lines 5 and 11 aren't needed, but shouldn't be a factor in the "screen flashing" you report here.
Do you see the same flashing when you use the latest release of Filemaker (11v3)?
I haven't had run it again yet - due for July 1, but will let you know :)
Also, check the layouts your script visits for any layout based script triggers. If you have a trigger like OnRecordLoad or OnLayoutEnter on one of these layouts, your script could be tripping that script trigger and its script could include a refresh window or other step that is causing your window flash.
One easy way to check to see if script triggers are interfering is to use FileMaker advanced's script debugger to watch the script execute step by step.