There are two areas for startup scripts in the Setup-->Run on Startup GUI, one for Forms ( .efm) and one for Scripts (.vbs).
You can use Visual Basic Scripts to run on DxDesigner Statup, but i think .bat or .exe is no supported format. The Tool expects a vbs script but can't execute e.g. a EXE directly.
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....but to save re-writing the scripts, you should be able to write .vbs that will call the existing .bat file! I've not tried it, but can't see why that wouldn't work!
Good suggestion Robert, I moved the topic to Automation and Scripting.
SavaGE, I haven't been able to try yet, but I will. Hopefully I will not bump into acces and security issues... Thanks for your suggestion!
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Have a look at this thread.
If you follow that example, you can add more items to the Load_DxDesigner.vbs file to do the things you are trying to do. That script will run every time you start DxDesigner. All vbscript functionality (such as file operations) can be done in there.
If you share a bit more about specifically what you are trying to do (and why) we may be able to provide further assistance on how best to accomplish it.