It seems that recent builds from SVN cause very odd errors for me. The first is that many ships lack thrusters entirely. They can still move, but they have no thrusters. I have no way of telling what ships will have thrusters and which will not (though it might only happen to ships that arrive after the mission starts - I can't confirm this though). The second problem was that Flak projectiles didn't detonate unless they hit their target, though this seems to have been fixed when I updated my build today. Another is that destroy wing directives can frequently not complete themselves. Even though all of the ships were destroyed, it will still say that there are a couple of ships left to destroy. I have experienced this but in multiple missions in two campaigns. The last, and certainly the weirdest, has only occurred in one mission so far. What happened is that an Arcadia in that mission (that was there when the mission started), spontaneously warped in a couple of times. After replaying the mission over and over (though bug #3 seems to keep me from finishing it), this problem happens again and again. The subspace hole forms at its former location, and it warps out of it, retaining its hull integrity etc. Its worth noting that that mission was red-alert though, and I didn't create a new pilot for that campaign. I am also going to take a look at the mission file to see if anything weird is going on.
EDIT: Well, the build I'm using isn't directly from SVN. It is modified to test the ship template code. I have experienced similar issues with standard SVN builds though.
And just to be sure, my system:
Macbook Pro, 2.4 ghz, Mac OS X 10.5.2, GeForce 8600M GT