I've got a command prompt application on my phone, and whenever I run the start command it always runs the file as a system process, and the executable never visibly opens on the computer.

How can I do this? When I run command prompt on my computer itself, with the exact same command, it opens the window as expected.

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Try:

runas /user:USERNAME program.exe

You will then be asked for a password for the user account.

EDIT: It appears that you are trying to run a GUI application, when you would need a RDP client for that, and not this remote command line program you seem to be using.

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updated tags. The application hangs and never receives a "reply" from my computer... – Cyclone Mar 28 '11 at 20:41
Unfortunately, I think the app would still end up on a hidden private desktop, even if that desktop belongs to the correct user. – Joel Coehoorn Mar 28 '11 at 20:41
@Cyclone: If the username includes a space, put quotes around the whole of the /user switch and username. – paradroid Mar 28 '11 at 20:43
@Joel: I am assuming that this is not actually a GUI application. If it is, the OP should be using a RDP client instead of a remote command line. – paradroid Mar 28 '11 at 20:47
@paranoid - could be, but he's looking for a window to appear. I don't think he'll ever see one. – Joel Coehoorn Mar 28 '11 at 20:48
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