Wouldn't that affect my entire 3DS Max install? For example, if I start a fresh scene it works fine again until it doesn't. It's just that file now that crashes on Ctrl + Z
Not sure what you mean by 'affect my entire 3dsmax install'. The ENU just holds your custom settings so when you move that folder (temporarily) then 3dsmax will load as per default settings, scripts/custom key bindings, menus etc will all be reset. My point is you can just do this as a test and see if ctrl+z is crashing on those projects. If so, you know that something in your ENU is broken. You can then go ahead and delete the new ENU and put your old one back so you have all your settings again and 3dsmax will return to how it was before you did this test (you need to do this while 3dsmax is closed).
Next Steps:
This means you have isolated the issue and its certainly related to something broken in your ENU. At which point you can decide to leave it or to start over and backup your key bindings, menus etc by saving them out from the Customize > Save Custom UI (and load them back in using the same menu after starting with a fresh ENU). This will save you some time regarding your UI, however it would then be wise to install your scripts as you need them (not all at once), this way if one of those scripts is the issue you will find out which one since you can just do a few ctrl-z throughout the day until you can repeat the crash.
FYI there is no harm in having multiple copies/backups of the ENU, if you are under a deadline you can just swap back to the one you need for all your daily stuff (even though its broken) while building a fresh one. I have about 5 different ENU setups for different clients which match their setup, this way I can troubleshoot things in their environment to replicate errors they are having.