"You are opening the application"..."for the first time" problem

Hi -
We recently upgraded to Mounatin Lion and when opening a couple of different applications (Quickbooks and Vectorworks) we often, but not always, get a warning message saying something like "You are opening the application ____ for the furst time" even though the application has been opened many times before.
I've seen a few older suggestions in the archives (pre Mountain Lion) that involve opening a Terminal window and entering some lines of code. Is that my only solution, or is there a file that I can trash or something else?
Thanks -

Having this exact same problem - Not just after the upgrade, but began a few months in.
Hope a solution comes up. Most tips online are from 2006 or 2009.

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