After installing SF and then re-applying the 1.12 patch, I had major issues with slow game response.

The fix was to reinstall everything.

Steps:

1] Backup your 'My Documents\Battlefield 2' folder.
2] Remove SF.
3] Remove BF2.
4] Delete the BF2 program folder that is left behind.
5] Install BF2 - don't patch it!
6] Install SF.
7] Apply 1.12 Patch
8] Copy your 'profiles' folder from your backed up 'My Documents\Battlefield 2' folder into the new 'My Documents\Battlefield 2' folder.

I then put a copy of pbweb.exe into the 'pb' folder in the main Battlefield 2 folder, and ran that to update the punkbuster. Get it from www.punkbuster.com

Easy as that.