This is a notorious issue with rain, but it's also caused ocassionally by other sounds. I worked around it by deleting the OpenAL files in bin/natives and installing them in my OS. Never had sound lag problems again.
I followed the steps from here: http://www.minecraftforum.net/topic/892045-sound-lagstutter-fix/
I'm sure this is also the cause of MC-46. The workaround I provided there also fixes this.