The only versions I have played are 1.2.5 through the current version and all of them have had the same problem. When swimming up against a current and you are drowning, each time you loose a heart and spaz out you loose height and this makes it impossible to get air and you die.
Can You describe it a bit more?
Also, I swear the knock-back effect when drowning is removed since 1.3.1…
When and where does this happen? In e.g. waterfalls?