I am trying to run a EXE or HTA file from command line, all it is, is a popup message that informs the end users of what is about to be deployed. I am run it from command line locally and it works great, but when I set it up as a task sequence it will not run.
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Have you examined the log file smsts.log?
Run the HTA using a Run Command Line step.
Here is an example: %SYSTEMROOT%\system32\mshta.exe %ScriptRoot%\MyCustomHTA.hta
You could refer to the sample from here.

Paladin Guo - MSFT
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