If you have not already done so, try closing out of PADS and restarting to see if that makes any difference. A similar issue to what you are describing with selecting objects in the Project Explorer can occur when you are in a verb mode such as adding a 2D line, working with component move mode, add route mode etc. If the problem persists close out of PADS Layout, go to Start > Run, type Regedit, click OK. Browse to HKEY_CURRENT_USER\Software\Mentor Graphics\PADS9_3_1\PADS Layout\Workspaces. Right click on the Workspaces folder and select Export, provide a file name and location for the .reg file. Right click on the Workspaces folder again, select Delete. Close out of the Registry Editor and restart PADS Layout.
Simply restarting cleared it up. Can't believe I didn't try that. Thanks a lot!