Launchpad Glitches
I have had some issues with Launchpad duplicating entries for applications I move or rename. I also had a bizarre glitch where applications/groups would have the wrong label or icon (usually the former), particularly after creating groups and/or moving icons around. A group containing the Adobe CS4 applications being called Xcode for example.
The only thing odd on my machine that I can think of is the copy of Adobe Flash Professional CS4 (so much for Adobe saying it doesn't work), which I got working by using the terminal command 'lipo' on the main executable inside the application bundle.
Though I do have Sophos Anti-Virus and both the Apple and Oracle versions of Java.
Other than excluding the database file from Sophos' on-access scanner, I can't think of anything else that may solve the issues.
iMac, OS X Mountain Lion (10.8.4), 21.5", 2.9GHz i5, Late 2012