OS X (Yosemite v10.10 and X Mavericks 10.9.5) switching between/selecting open windows after scansnap v6.3 L23 upgrade

Mid-2013 13" MBA w/1.7 GHz Intel Core i7 running Yosemite. ScanSnap auto update ran this evening (02 Nov 14) and upgraded my ScanSnap manager to version 6.3 L23. Immediately after the update the OS started making different open windows (Safari, Finder, Mail, etc.) active for 1/10th of a second each. I could select a window but the OS kept making other windows active. I had enough time to click on one item or type one letter before the OS would make another window active. It was so bad that I couldn't even open safari and conduct a search. I finally used Time Machine to go back ~1/2 an hour and that seemed to find my problem.
Not long after I stopped pulling my hair out, my wife started complaining about the same thing. Mid-2014 MBP Retina running Mavericks 10.9.5 (I hadn't updated her OS yet). ScanSnap updater ran and updated her ScanSnap manager to v6.3 L23 and she had the same problem. However, she had unplugged her USB Time Machine backup drive so I couldn't restore her computer to a previous time. I have tried resetting PRAM (three times), uninstalling the ScanSnap software via safe mode, checking for errant processes via Utility Monitor (none identified) and am now in the process of updating the MBP to Yosemite.
The best way I can describe the problem is the OS just keeps activating/selecting different windows. When no windows are open and no programs are running everything seems fine, then when I open only one item (a finder window, for example) the OS starts select it, then not, then selecting it, then not, etc. If I open more than one window/app it seems to rotate through them. Problem is that no matter what I do the window I select does not stay selected.

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From: [email protected]
To: [email protected]
Subject: After trial version expired and purchasing creative cloud membership programs still will not open
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sample.seq ‏10 KB

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OS X (Yosemite v10.10 and X Mavericks 10.9.5) switching between/selecting open windows after scansnap v6.3 L23 upgrade

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