I am using an arduino pro mini 3.3v with the MS5541, and I think that the problem may be that the 3.3v version operates at 8MHz instead of 16MHz. I will try to put it on a scope and play with the timer values for the pwm, but I don't know if I will get anywhere. I havn't been able to find any tutorials about it anywhere.

I think that the other option will be to try to put a 3.3v reg on a 5v arduino and see how it works for me.

http://mewpro.cc/2014/10/25/yet-another-3-3vizing-an-arduino/