KACE Product Support

Becuase you chose the KACE Product Support tag, I'm going to assume you are refering to the AppDeploy Repackager. No matter the tool, you can't really capture an uninstall as an MSI-- you'd need to do that separately. That said, you don't have to run an executable at all, you can just make whatever changes you want and then do the second snapshot to capture any changes made to the MSI.

I am using wise package studio to create a snapshot, but is almost the same for all tools. After the initial snapshot the tool is asking to select an exe or a batch file to execute before to run the second snapshot.

I never use this window to execute the installation, I am executing the installation double  clicking on setup. Or if I want to modify something on Windows or install a software manually in Program Files (just copy the file there and create the shortcut), I am doing all this using a file manage or Windows Explorer. So the answer is, just ignore the window where is asking you to specify the exe file and perform the modifications on your Windows or remove what ever you want and you are done just click next and execute the final snapshot.

You can restart the computer if you want and after that start the tool again and execute the snapshot, the tool will ask you if you want to re-run the initial scan or if you want to perform the final scan. You have to perform the final scan.

thanks for your answer, yes you are correct, it is the appdeploy. I did manage to do the following, start the snapshot, uninstall the package, it prompts for a reboot, I do so, and restart the appdeploy application, it prompts me to continue or start over, I choose continue, then do the installation of the new package, re-snapshot, and that seems to do the job. It seems to capture additional things that makes the package misbehave.