Unfortunately, i have the crew-on-bridge-while-underwater-problem myself, and my first patrol ended in tears as my co2-levels went banzai while surfaced, and my men died.
Tried a new patrol now, and found that the crew leaves the bridge (and come back when I surface) if I DONT save the game and reload OR alt+tab. Finished an entire patrol from Penang and back with lots of lurking about looking for the Allies, and no problemos. (Besides my expensive Falke torpedo going boom approx 400 metres from my boat
)
PS: I still get the old stuttering if I let the game run on both cpu cores, but if I limit it to one, it runs like butter. The game looks awesome, runs great and that IXD2 is one beautiful 3D model. Hooray!