I'm not sure if the depth matters when your below the thermal layer, What usually works for me is doing a fast steep dive (full or flank) until I hit the layer. Cut to slow (or silent if I still have a couple fish loaded) and do a hard turn and level out about 50 feet under the layer. Then I adjust the course on whats going on above, sneek away. If there's only a couple escorts I'll come up slow and try a shot with the aft tubes.
I wonder if one was just above the layer doing full back then dropped below the layer and went to silent running ahead, if this would mess with the AI