This freeware tool may come in handy for you:
http://www.12noon.com/reschange.htm
And then change the OOTP shortcut to this:
reschange.exe -width=1024 -height=768 "C:\program files\sports interactive\OOTP Baseball 2006\ootp2006.exe"
...in theory, that will force your computer to change to 1024x768 while OOTP is running, and then switch back when it's done. I haven't tested it, so try that at your own risk.