Interesting. That's very interesting... one way to solve it would be to get a clean slate and reapply everything until one either finds the source of error, or everything works... however, that would take too much time to preform optimally.
Edit: Wait a minute... that seems familiar, the inability to interact with certain objects in the world; i.e. terrain blocks, is consistant with being in Adventure mode. If the permissions were tied to gamemode, then I think that Adventure would also be equally restricted from using plugin commands. However, if this extends to the use of tools or chests, objects that DO work in Adventure, then that isn't the issue.