Windows 7: Problems after mounting HD in external drive and then reinstall in PC

Yesterday, I removed my hard drive from my PC (keyboard was broken) and installed it in an external drive. Today, after fixing my keyboard, I reinserted the hard drive. several weird things happened:

1. Google Chrome is gone.
2. I can't download anything from any sites
3. i can only use IE as a browser, and can access many sites, but can't access gmail
4. When I try using Skype it says that I cannot use it because I am logged in already on the computer.
5. "My Documents" folder seems to have disappeared.



I suspect it has to do with when I mounted the drive in the external drive and connected to the other computer, I had to do a "one-time" granting of permissions to see everything on that drive.

Any idea how to make this all back to normal? I tried a system restore to a known good point prior to the mounting as external drive, and the problems remain.

-Derek