Ok, I believe I have resolved the problem. Previously, all playable hull sonars' max height were set to 0m (ok), but all the sphere and TA sonars were set to 300m. According to my understanding of array geometry, max-min shouldn't affect the operation of it in the cone.
So, I have changed all playable passive sonars to have max height of 10m and min height of -3000m. I found that if I set it to 0, then even in low seas contacts would not display correctly on the waterfall. I have changed the hull sonars as well, in order to be consistent. In addition, I have changed the sonar buoy parameters to match these as well, to eliminate the same skipping problem.
Everything seems to work and the seaskimmers don't show up on sonar anymore.
I and a few others need to play around with it a little bit more to be sure I haven't messed anything up. If anyone wants to look at the fix, send me a PM. :|\
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LW
 
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