Change window position from config file?

[HyperActive1DUK]

When running applications through this tool using the 640x480 compatability setting, the application opens in the top-left corner of my monitor, but is aligned to the client rather than the window. As a result, the title bar is not visible and part of the window cuts onto my other monitor. This can be fixed by using the Win+Down hotkey, however moving the application window after launching the program seems to cause graphical errors. I'm wondering if there's any way I can accomodate the full window upon launch? Setting co-ordinates or centering the window upon launch should also resolve the issue.