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Most likely because you upgraded instead of a clean install. I suggest you backup everything with an external hard drive and clean install Snow Leopard.
To clean install Snow Leopard do the following:
1) Insert Snow Leopard disc and restart computer while holding down the option key
2) Select the Snow Leopard disc then click continue once at the beginning of the installation until you see the menu bar at the top
3) Click on Utilities, then Disk Utilities
4) Select the root directory (Not the one that normally says Macintosh HD) and click on the erase tab
5) Click on security options at the bottom and select Zero Out Data and name you hard drive whatever you like
6) Just click erase and wait for it to finish
After it's done just close the Disk Utility and continue on with installation as normal
 
Before reinstalling the whole OS, try a permissions repair and verify the disk.
 
Certain extensions do not work.

By the way that's a key stroke logger, did you install that?
 
Ok, so I did a clean install of Snow Leopard. Now all the apps on my iTunes are gone, so I sync my iPhone with iTunes and it deleted all my apps, is there a way I can get them back without having to download one by one? Thank you
 
Ok, so I did a clean install of Snow Leopard. Now all the apps on my iTunes are gone, so I sync my iPhone with iTunes and it deleted all my apps, is there a way I can get them back without having to download one by one? Thank you

You should be able to get the apps for free if you download them with the same account (because you already own them), but I'm not sure about bulk downloading the whole collection.
 
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