Difference in API calls in Windows 98 and Windows 2000/XP

[FalkonIsBack]

I wrote a program that uses common API calls like GetWindow, GetParent, OpenThreadProcessID, etc..Well the program works fine when running it in Win 98 but when I tried to run it in XP and 2000, it doesn't give any errors, but it's not running like it's supposed to. It runs a program that runs in a DOS window, so my program shells out to the DOS window and automatically runs the program. The DOS program waits for user input to continue. My program makes API calls to wait until the DOS window is closed to run the rest of the code, but it doesn't wait in XP or 2000..Can anyone help me????