I hate it when /home takes me to an area slightly above/below where I'm meant to be, and I die in the terrain and lose all the stuff I'm carrying. Then when I go /back, I can't find the items.
Just move your home point or make your home point not somewhere underground with very little space. If you /sethome dig around above and below a bit to give some extra room.
So you were looking when we executed the command - but what about when the plugin was first loaded - might be a message that appears then?
(Not sure how plugins are loaded; might involve a server restart?)
When your changing permissions, are you doing that via typed commands?
If so, is there also a config file - maybe that file has become corrupted/invalid in some way, meaning that certain permissions aren't sticking (although then I guess we should have the "no permission to do this" error when trying "/time day", instead of getting no response).