Every time it rains I seem to have problems boosting...I think water is getting on the filter and causing it to break up. Anyone have any other ideas on what it could be?

It only happens for a few seconds or until the next pull then it's fine

 

What kind of filter? Sounds like you already figured out your problem. Have you ever felt your filter to see if it was wet? It would probably dry out pretty quick under boost with the suction power of the turbo.

 

I have an apexi filter

 

I think you need to check your spark plugs and wires.