i doubt this is actually related to the emulator, it just doesnt sound like a problem it could cause. more likey, you are forgetting a part or something within of the sequence of events that particular cutscene follows.
do the scenes towards the bottom of the following link play though like they normally should? like does it actually show the airship flying towards that area on the overworld map or does it not show that either?
RPGClassics.com - FF6 Walkthrough v2 - Uncle Ulty's Portrait Session
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