Did you do any Time Compression? Did you dive deep and come back up? I'm wondering about that TC again... I'll load the mission up on my other computer and try it here in a bit...
Edit 1330: Well, I've done the same mission on the i3 laptop, and while everything appears to function as intended, I never did pick up the Yamato on radar. Got the sonar at about 1030 mark, 30 minutes in, but never got a radar, and then I got the visual from just over the 13k range... No sound issues though this time... I'll try again on the quad core after I re-install tonight...