Lyle,
Which "spyware" scanners? ...or hopefully "malware" scanners?
Do You have active antivirus app running? What is it's name? Is it updates automatically, and frequently?
Is windows autoupdate on and fully updated?
Is this a new system or did this problem just start occurring suddenly? if the latter, then when?
Assuming you can somewhat pinpoint ~when it started, was any software installed around or just prior to this time? Think hard..anything?
Does this happen from the moment windows is loaded until shutdown? with everything you do?
When a window in the background is flashing does the taskbar button change in color?
Do you mean dropdown menus in the flashing window only, or all windows? and you do mean drop down menus AND Taskbar menus? will it "pop you off" the start menu as well?
Are you certain it's all types of apps and not just that you usually only use a particular one (like an internet browser, usually)?
Lets say notepad, calculator and a windows explorer window (any folder) are open in that order, what happens? then close all and repeat. same exact problems in the same order every time you repeat? ..or does it randomly just start at some arbitrary point, which differs with each repeat?
if your opening menus by clicking once on a menu (i.e. Files) and then moving the pointer over the selection and clicking it, try a different technique: move pointer over the menu, press and HOLD DOWN left button "drag" the pointer into the list it should highlight the menu items as you hover over them. As long as you hold the button down is it holding the menu open now?
My apologies for the barrage of questions, but the clearer the problem is presented, the more likely that I or someone else can help. Just answer as many as you can, and as briefly as needed to be clear. It certainly sounds like malware of some type, but could be some type of conflict between software that you have installed, esp. a program that starts when windows boots. We may have to take a look at your startup programs and/or active processes to see whats going on. Make sure you describe the a/v software and scans you ran.
Thanks,
Mike