I don't mash with the lid on. While I agree that I may be getting air in from between the walls, I'd like to fix the problem of low flow first and see if that's still an issue. I don't have a problem of sucking air (or having cavitation) until I have wet grain - so I'm sure the issue is grain...
I've been having the same issue, and after reading this post stirred along the bottom of my MLT against the false bottom. Voila, my pump volume immediately increased to normal operations. It makes sense that I don't have the issue early on in the mashing process - it doesn't begin to happen...