I'm having a similar problem. When I first start out on a patrol, when I get a plane contact, I first check the weather to see how high the waves are; then I raise my SD antenna and dive to a depth where I know it'll be above the waves. Once the plane passes me again on its return leg, I surface. But after awhile, when I try this trick, I lose the contact after diving, even though the antenna is above the waves, as before. Sometimes raising my depth a little more will reestablish contact, but I still lose it again way too soon.
On this last patrol today, the problem kept coming and going. Sometimes it worked fine, sometimes it didn't.