Sorry to be quoting everyone again, but while we try to figure out the issue, we found a possible solution.
Going over different forums we found that it could be an issue with the persistent save. The solution offered there was to delete the persistent save file from the renpy save folder (both the one in the game folder and the one in %appdata%). We were not able to reproduce the issue, so we can't test this solution at the moment. If any of you can, and it works, please let us know.
Here's the link to the mentioned forum discussion:
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If it doesn't work, please send us the log file created when you try to run the game. It's a txt file that gets created when you try to run the .exe file.
If anyone needs more info on how to find and delete said files, let us know and we will write up instructions to find them.