Try repairing permissions (in Disk Utility), as this may be the cause of a number of your problems. Also try deleting preferences and related files.
Go to your home folder, then Library. Delete the 'Acrobat User Data' folder. In the Application Support folder, delete 'Adobe' (I'm not sure if this is Adobe Reader or not, it might be Photoshop things). In the Preferences folder delete com.adobe.Reader6.0.plist. There might also be a few other files here beginning with either Adobe or Acrobat.
By the way, why are you using Adobe Reader? It certainly had advantages over Preview in Jaguar, but the Panther version of Preview is, IMO, much better (faster, simpler interface etc) than Adobe Reader.