You know I love watching people gnashing their teeth over this subject. It (and a few other minor items) are inherited behavior from SH4. Seems like most people here aren't aware of that for some reason.
So here's the short version:
After 196 -200 meters (or 600 feet), there's this magical barrier you pass where the submarine's pumps can't keep up with the leaks. As i recall from watching the development of the NYGM anti-hummingbird mod, your sub is always leaking. This particular behavior, is inheirted from SH3 to some extent. You don't see this because a leak below a certain amount is not reported on the damage screen. So as you cross what i refer to the 200 meter/600 foot barrier, your boat loses boyancy and starts sinking. The only way to stop the decent, is to accelerate to flank speed.... err im sorry.. "extreme speed ahead".
Order rise all you want, but your boat will not move to a shallower depth until you blow ballast, thereby increasing boyancy. Reduce your speed , and you start to sink because you have too much negative boyancy. Hency why i say, pumps can't keep up with the leaks after 200 meters. (edit: supporting evidence is behavior in trim gauges. They peg out after 600 feet) How to adjust the pump rate? I never did figure that out, or even if it's possible.
An interesting side note is that crash speed (at least in SH4), seems to have an effect on this. (
http://forum.kickinbak.com/viewtopic.php?f=70&t=1885 )