I believe the license checkout doesn't happen until you try to open or start a project. Check your license setup, go to (in my case) C:\MentorGraphics\PADSVX.1.2\MGC_HOME.ixn\bin and run PCLS_OK.exe to see what licenses you are pointing too. Remove any unnecessary license pointers as anything extra can slow you down drastically. Be sure to check for anything using the LM_LICENSE_FILE variable as even if it isn't a Mentor license it can still slow you down, in this case find out what software is using it and move it to the correct Daemon variable.
Hope this helps.