Issues after using an external hard drive.

I have a 15 inch macbook pro bought in mid 2009 and never had a problem with it till I decided to backup my files to an external hard drive. I plugged in the hard drive last week and now when I startup and login to my account my mouse often doesn't work (clicking won't register and I can't click on ANYTHING) and/ or the dock (which I have set up to hide) will not appear, forcing me to hold down the power button to restart my laptop. Restarting in this way sometimes works and puts everything back to normal. Anyone have any suggestions on how to fix this?
Additional information:
The hard drive I bought is just a WD passport that I erased through timemachine to format it for the Mac system.
I also have antivirus, have done a scan and nothing pops up.
I'm running the most recent version of OSX Lion.

It should be as simple as just setting the library location on each computer to read from the external drive
It is.
Sounds like you are referring to the *iTunes music folder* location in the prefs. This is not the same as the iTunes library.
The iTunes library file is located by default in \Music\iTunes\ on yoru boot drive.
This is all the info about what you have in iTunes. It is also the default location for your music but that can be changed in iTunes prefs -> Advanced -> iTunes music folder location. Changing this will change ONLY the location of the music, not the iTunes library.
Powerbook has no problem reading the iTunes Library on the external.
Great! Do this.
Connect to the drive Powerbook.
Copy the entire \Music\iTunes\ folder from the PowerBook drive to the external drive.
Hold Option and launch iTunes.
Select *Choose existing library* and select the *iTunes library* file in the *iTunes folder* you just copied to the external.
Everything should work.
Go to iTunes prefs -> Advanced and set the *iTunes music folder location* to the iTunes folder you hust copied to the external.
Tick *Keep iTunes music folder organized* and tick *Copy files to iTunes music folder when adding to library.*
Now go to File -> Library -> Consolidate.
This will copy everything in iTunes, into the iTunes music folder in the iTunes folder you copied to the external.
Quit iTunes and plug the drive into the other computer.
Hold Option and launch iTunes.
Select Choose existing library and select the *iTunes library* file in the *iTunes folder* you copied to the external.
Everything is there with same playlists, ratings, date added, artwork, etc.
That's it.

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