When I click links in another program, they do not work

I often use Skype to talk to friends, and Twhirl for Twitter. Typically, when I click links in these programs, they open in Firefox. But, last night, Firefox crashed. When I started it back up, Windows asked is I wanted to allow FF to make changes to my computer. I said yes, figuring it was updating something.
After this, when I clicked a link in Skype, it asked if I wanted to allow changes to my hard drive, again. I click yes, and the link would open. But, whenever I click a link in Twhirl, nothing happens at all. And even Skype isn't doing anything, just like Twhirl.
I've tried restarting Firefox, Skype and Twhirl, and my computer itself with no luck.

Make sure that Firefox is set as the default browser.
See [[How to make Firefox the default browser]] and http://kb.mozillazine.org/Default_browser
Check that you do not run Firefox as Administrator.
Right-click the Firefox desktop shortcut and choose "Properties".
In the Compatibility tab, make sure that Privilege Level: "Run this program as Administrator" is not selected.
You also need to check the Properties of the firefox.exe program in the Firefox program directory.
If you can't make the changes then you need to start Windows Explorer as Administrator.

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