This one's cropped up with the latest patch. I reported this in the "known issues" thread, but felt this needed a bit more exposure and info, as it's a game-breaker for me.
Basically, regardless of whatever I set in the options, the game appears to have auto-turn and skip remaining automoves enabled. Before, I was perfectly content to just hit the Turn button after I was finished, now it rarely gives me that option. It doesn't even blank out the Turn button as it's forcing the turn advance, as I assume it's supposed to (to indicate that it is, in fact, advancing a turn). Furthermore, each time the game advances, some of my ships aren't given their moves, they just sit at their last position. I had a constructor set to move to a resource only about four moves from its starting point, and it sat on its second move for three forced turns before I realized it wasn't going anywhere (even though each turn, it supposedly had all its moves remaining).
One thing I've noticed is it always triggers a turn advance if I have nothing remaining in that quick notification sidebar on the right, after loading a colony screen and clicking Done to close it. The same happens if I click Build Ship instead of Done. As long as I have something remaining on that sidebar, it acts normally.