Well if your scene is now 6 minutes faster to open it means something is broken in your ENU which contains all your UI settings as well as other scripts and things that you normally rely on.
You could try this:
Paste back your ENU folder that you backed up to your desktop.
Load your scene... which will take awhile since obviously something is not functional
Now in 3dsmax do the following:
Customize > Save Custom UI Scheme > save this somewhere
If you have made your own custom hotkeys then:
Customize > Hotkey Editor > Save as > save this somewhere
Then delete that ENU folder (keep the backup incase)
Start 3dsmax as normal, it should look like defaults.
Select Customize > Load Custom UI Scheme (pick that file you saved)
same with Hotkeys
Restart 3dsmax
You should now have a clean 'ENU' with your UI you are used to.
If something is missing I highly recommend you install the script 1 by 1, reload 3dsmax each time and see if your load times change. If they do its probably related to the very last thing you installed which means you need to investigate/contact the author of that script.
Edit:
To answer your previous question, yes the above settings is what I do to save my UI and hotkeys (toolbars, hotkeys, quad settings, asset tracker etc.). I keep these in a folder in case my ENU gets corrupted and then reload these when that day comes (because it will). I also keep a copy of a working ENU folder for the same reason, since there are other things I'm not aware of in that folder that can possibly be corrupted at a later state... thank you very much Autodesk. So long story short, keep that UI saved, keyboard shortcuts, and the ENU when everything is working well. When the time comes just delete the broken ENU and replace with your saved ENU, if that fails then at least you have the UI and keyboard shortcuts saved separately (without your scripts, the toolbar buttons will be there but they are linked to a missing script, which as I mentioned earlier install 1 by 1 as you troubleshoot).
