Jack, my experience with this issue does not exactly match yours. I have numerous scripts that freeze the window, change layouts to a different window based on a different table and back again with no flash in either windows XP or windows 7.
I DO get a flash with the New Window command and it's quite annoying at times.
I have found the following script steps trigger a window refresh
Refresh window (duh)
Freeze Window (this can be a suprise and if one script freezes the window, changes layouts, then performs another script with freeze window as the first step...)
And while I haven't tested it, I wouldn't be suprised to find a few other steps that manipulate the window such as GTRR with the new window option that might also cause the flash.
Have you ever considered offering your design services for free to me? :)