Without the QVW file, rather difficult to look into things, as the only logical thing would be something in the script that is not being handled by Publisher, but without access to that information, no way to confirm... If you need to scramble any sensitive fields, you can do so via the Settings\Document Properties\Scrambling tab, only way I see for you to get further feedback on this one. Also be sure your Desktop Client version matches the Publisher version and I would also confirm the QVB.exe that is attached to Publisher is the correct 12.40 version too, things need to be in sync, only other thing of which I can think is something is out of sync somewhere that might cause the behavior.
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I assume that most of variables aren't manually set in the script else that they are loaded from included-variables, per loop through external db/excel-source created variables and/or calculated ones. If so it might be the wrong ones loaded and/or the creating/calculating-logic doesn't work like before. Therefore I suggest to check these logics.