When 5.4 was installed, did it update the APTPATH from 5.2 to 5.4 (i.e. C:\Arbortext\Editor to C:\PTC\Editor)? Do you have apps dependent on the APTPATH being set? When we moved to 5.3, I took those out of our environment vars without any ill effects.
When updating from 5.1 to 5.3, I was seeing really strange behavior and odd errors/startup times, and found that my old Arbortext.wcf wasn't "valid" when 5.3 was trying to open it. Completely deleting it and restarting Editor to generate a new one seemed to do the trick.
If your organization is anything like mine, standard users have little to no access to write files to their C:\ drive. Is it possible you might have a R/W issue?
Just trying anything I can think of at this point...
Personally, I wonder if it's an issue with the license manager--maybe it's trying to check something over a network connection that isn't there and it has to wait a while before it times out--but I don't know, and our licensing expert is out this week.
Some other developers suggested trying to use the -nohc and -nojvm flags on your start up command (see help 5717) to see if that makes a difference.