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Message boxes and windows not displayed

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Running an AutoIt program on Windows 2003 Server x64. Program is launched remotely using rexec command. Connected to server via Remotely Anywhere to display the console.

Program starts but message boxes and windows are not displayed. Program eventually times out waiting for a window. Shortened the program to troubleshoot... message boxes and windows began displaying. Shortened the program again... message boxes and windows stopped displaying. The original program does run successfully if launched from the console using Remotely Anywhere instead of using rexec.

Any advice on how to solve?

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