Simply put, Lairs seem to be a bit screwed up. Despite having the requisite points for the next tier of The Beast Lair, it never upgrades. Logging off, closing the program, leaving the whole area where the Lair is located entirely and resets don't seem to do anything then eat up lair points.
I'm not sure if its just the Beast Lord Lair or all Lairs but since EE came out its been stuck in limbo.
No bug found. However - fixed bug which caused the tunnel not to be removed at logout.