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[Kas Ob.]

I doubt that Process Explorer or Process Monitor will help at all.

The fact that the command is running fine when typed by user (direct input) in the console (CMD), means some sort of isolation had taken place.

So it is either some policy and/or the user isolation is in effect.

OP failed to mentioned what type of application is using, standalone or Windows service ?
OP didn't share or screenshot the exact error message !

So it is more guessing than real investigation.

One thing though might help :
Run Process Explorer as Administrator, and get the User running that application from the Image tab, see if there is something wrong.
Also from Process Explorer, compare the Security tab of your application with the CMD (cmd.exe), see what is different.

After these suggestion, we might have better picture, and someone might help you solving this.