Created a new Nausican char on Tribble. Same issue: no flickering door to exit Great Hall. The only thing I can think of is that these were Klingon side characters that A] weren't my first Klingon character, and B] were created after an intervening Fed char was created.
I am having this issue as well. None of my Klingons can enter the courtyard from the great hall. It is extremely annoying and about to get even more so when season 2 hits as there is a mission that requires going into the courtyard.