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EDIT: That still does not work on mine I can only make a bluetooth connection after the full boot.
I think at early stages of boot, drivers are not yet fully loaded.
Hmm perhaps I misunderstood what you meant byIf that means as a secondary adapter to the one built into the Pi3, it's a completely different issue. My earlier comment was for connecting to an adapter from the Pi, where the adapter is connected to the mount as an EQMOD direct bluetooth interface.
If I can throw my own 2 cents, I had the same symptoms on an EQ-5, and it was definitely the cable which was not plugged securely enough. OK EQ-5 is using a RJ45 plug, but it appeared that even a small electrical disconnection during rotations was causing a desync in the tty exchanges, which only a disconnect/reconnect of the driver, thus a close/open of the device port, would solve. It is very tricky to diagnose physically actually. Currently the eqmod driver isn't covering that failure situation (fail exchange, try close/open).