Same thing happen to me and this is how I fixed it.
I cloned my OSX HD to another drive and booted from that drive. I erased the OSX HD drive and reinstalled OSX 7.0 that I had saved to the 2nd internal drive. When asked to copy my System and Home folder I used the copy of the OSX I had just made to copy them from. Skipped the Set Apple ID since I had this on the clone. After the installation was finished I repaired my permissions. Went to the Apple logo in the Menu and clicked on Software Update. After the update was finished I clicked on the update again to see if there was any more updates to do, there was one more. Repaired permissions again... I notice that the update did not ask to installed Safari 5.1.7, I still had 5.1.6. I downloaded the Safari update from Apple's site... This took about an hour to do and my iMac has never ran as fast as is is running now.
Safari update 5.1.6:
http://support.apple.com/kb/DL1531?viewlocale=en_US&locale=en_US
One side note; if you have any iDivices for example the iPad. And you sync and do backups to iTunes byway of wifi. You will to hookup the iDevice (one time) to the Mac so iTunes can recognize it.
I use the an app called Cocktail and I think it mess with System files (caches) that made this happen. OnyX is another popular program that a lot of people use. I made a test with my default settings in Cocktail and sure enough my dock URL icons disappeared. I did another test with amended setting and they didn't disappear. Of course this took some time to finger out. I'm going to send an email to the people who make Cocktail and explain this to them. (They had an update yesterday!!! Go figure…)
So, if you use Cocktail or Onyx you might want to hold off using them or some other program of this type. This worked for me, your milage may vary.