In all modules EXCEPT Order Entry I am able to see our groups and update settings as normal. When going into OE all of our groups seem to be missing, however all users are assigned to these missing groups.

Not sure what caused this issue? Logging in as a regular user, or SYS does not allow me to see these. V# 8.1E(120907)

Security Groups are set up individually in each module. For instance, Payables could have 5 Groups and Order Entry could have 2 Groups. You just need to add OE Groups that correspond to your users. If there are no Groups set up in a module (as in OE in your case), all users have open access to all functions in that module.