Not exactly sure WHY this happened but this is the deal...

I added a Rank to our site, and deleted an older rank that was no longer in use.

When I did that, the permissions for everyone changed. Things they used to be able to see as an applican't they no longer could, the Guild Leader could no longer manage events (only the admin could), etc. If adding or removing a rank changes the entire workings of the website, then it is not a good thing...

I went through the same thing when I first designed my site.

This led me to delete all of the ranks and recreate them with the following format. My solution was to setup a bunch of rank placeholder names, and space them apart far enough number wise, so that I could add between them later and not worry about it.

Example:

1 - Site Admin
2 - Guild Leader
4 - DKP Officer
10 - Officer
15 - Class Leader
20 - Member
30 - DKP Bot
40 - Bot
50 - Probation
60 - Guest
70 - Wall of Shame
80 - Pending Invite
90 - Inactive Guild Leader
91 - Inactive DKP Officer
...
98 - Inactive
99 - Non Member

The stupid thing is the Guild Leader is the 2nd rank (below admin) and I deleted a rank like 6 levels down and added one in its place and it removed all of his permissions.

That's very odd, and I'm sorry for the trouble. I don't actually have an explanation for that. I'll have to see what I can uncover there.