Did you install SC in the default install location under Windows 7? (iow in c:\Program Files\Electronic Arts something\Subcommand)
I suggest you do not install (any game to be modded) in there. Any file changes the game makes in there , like in the Scenario folder, or application of the SCX/SCU patch, might be only temporary or not applied at all due special protection of the Program Files folder. Assign your own install folder outside of it. Then you do not need to run as admin, nor do you need to use the compatibility option.
Do not forget that you need to execute some .bat files to make the SCX/SCU patch complete.
I can get the stock game running in Win7 without a problem. Caveat: I do not have SCX/SCU applied at the moment. But I think I did have it in the past.
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