I just recently got GroupManager and everything was working fine, permissions, prefixes and factions all going smoothly. I was on my server and my Admins were telling me to add certain commands that I hadn't added yet. So, I went to the config files and gave everybody more commands and I didn't want to restart the server because there was a lot of people on, so I went back and typed /reload and people went from having permissions and prefixes etc. to having nothing. No permissions no prefixes nothing. I even noticed did not have any perms so I opped myself again to make sure I was op and I still didn't have any permissions not even /spawn. So this is really and If anyone knows how to fix this that would be great. Also I tried re-downloading groupmanager and that didn't work, everything saved from when I deleted it and it didn't work at all.
/reload isn't always a good idea, always restart when possible (even when you're not using PEX) as for the permissions, iirc GM has a tendency to delete perms when configured incorrectly.
I had this happen to me too. You probably made an error in the file when you wrote the new permissions. If you are using notepad++, be sure not to use the indentation provided when you hit enter.