I tested this out and am able to reproduce it nearly every time.
When running short of breath and swimming to the surface, the player soldier continues to choke until the camera is moved above sea level, even though the soldier's head is out of the water. This may be an engine limitation (stabs in dark) there are also occasions when bringing the camera above sea level, the soldier is still unable to breath.
This is not the case when swimming to the surface using the X key
Test Footage:
http://www.youtube.com/watch?v=XrrLN0hDfCw&feature=youtu.be