I've been following this thread and been doing some testing myself. What seems to be working for me right now without changing much, aside to the sequence is changing the SSID before starting Karma.
On initial start-up the device broadcasts "pineapple" with Karma off.
I change the SSID and get the successful message, I notice the broadcast SSID changes to what I've specified and no longer see "pineapple".
I then start Karma and noticed that the new broadcast SSID changes back to "pineapple", but through the hostapd_cli with the get_config, it does reflect the SSID that I specified.
Approximately 1 minute the new SSID begins to broadcast.
I've repeated this process multiple times and appears to be consistent.
Not sure if it's a sequence issue here or if it was initial designed to be executed in that manner before Karma starts.
Curious if the sequence helps anyone else, but prior to trying the sequence I was messing with the permissions of the "hostapd" directory, but reverted back to it's original state.