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The Good: I can run SWBF2 in safe mode if run as administrator.

The Bad: I can't run normal SWBF2.

The Ugly: SWBF2 wants me to update DirectX, which I already have so when I press okay and agree to terms all it does is say your DirectX is ready. I have restarted the computer, so any updates it did should be fine.

Anyone know what's wrong?

The only way I could get SWBattlefront II to work on my W7 machine without admin rights, was to turn off User Account Control (UAC). You don't really need it if it's your personal computer.
Go to this directory: Control Panel/User Accounts and Family Safety/Change your Windows password/Change User Account Control Settings, move slider to never notify, click OK, and reboot.

I hope that helps.

Thanks, that will help with the pop-ups and all, but that didn't solve the issue.