I was pretty sure someone responded to this in-game or on the forums but from the looks of it, this has not been resolved.
Qembek, you mention that you repaired a stone. Did you repair both stones?
"While alive, an indestructible barrier blocks access to the first barricade of the fort. This barricade vanishes once both Guardian Stones are destroyed. The guardian stones, unlike the Emperium are vulnerable to normal attack and supportive skills. The guardian stones can be revived at any time by bringing the proper items. If both guardian stones are restored, the barrier will again reactivate. Note that even though the barrier will block access to the fort proper, enemies that have already passed this barrier when it is restored are still able to destroy the other barricades and potentially destroy the castles emperium"
The WoE scripts have not been modified in regards to these things, and if bugs in this script do exist, they should exist on ALL servers as it is an eAthena-owned script, not an Amistr-based script. The original issue when you first experienced problems (when WoESE was cancelled due to false-starts), was an unrelated issue in which the system failed to restart WoESE and instead started WoEFE during that time. The emperium was still available which led to the primary issue back then due to the way the castles are spawned on reloads when unowned (also due to the transfer issue during that WoE). Those issues have been mitigated with a backend re-script of the transfer system.