Have you tried the ol' standby, repair permissions? That's usually a first step in quirky problems like this. To do that:
Go to Applications/Utilities
Select Disk Utility
Select the startup disk and click First Aid
Click Repair Disk Permissions
Quirks like you're experiencing often happen...
We gather here to remember an old friend.
I was close to him; in fact loved him. Oh, he could be fickle. He had an odd way of remembering things. He would sometimes just stop working for awhile. Some of that was probably my fault; I kept giving him more and more. Extensions, Control...
Go to System Preferences (either choose the icon from the Dock or go to Apple Menu > System Preferences. Click on the Classic icon, then uncheck "Start up Classic on login to this computer"