Sadly, I can confirm that there are still "cannot end turn" bugs. I have a save game that was created from a game started with 3D, so it isn't a hold-over from a save in a previous version.
I think it's a different bug and it's been sent in.
In this case, I had gotten a "Krynn are growing more and more powerful" event and a 50% speed increase event (Ultradrive?). I was building Large hulled ships to take them out anyway, so I sent my first ship their way to start laying waste. After it arrived, I tried to move it and couldn't. It had 2/6 Move left but wouldn't do anything and I couldn't end the turn (but the button was visible).
I coaxed it over by moving less than its full allotment and finally attacked some Krynn ships, leaving me at 3/6 after a short move and one attack. This resulted in the same "Turn button visible and flashing, but can't click it" as above.
I'm hoping I might be able to work through the game saving after short hops, never using more than the built-in engine amount and maybe that'll get me through. I'd like to finish this particular game