It happened when i was duo krex with my buddy. When we finished the first run and left the map , my BM dced immediately. After relog , i noticed my BM was sent back to CBD instead of staying in Ruins of Krexel I , and the portal blocked me with the message "You can only enter twice a day".
Logging out in the boss map returns you to CBD, that's not a bug. Your character AstroRanger has entered twice today, relogging or a dc would not affect this in any way. Based on the details you have provided I can't see any problem here.
I clicked the NPC to leave instead of log out by myself in the boss map. When i pressed the "Yes" button , the screen went black and returned to the log-in panel. It's weird cuz i'm quite sure that was the first krex run today. Sry for not providing enough proof to explain this issue, but it never happened before since i joined RMS.