Same problem here. In my case it happens mostly when playing Chernarus in MP. I host a mission to play along my brother (client) and I get really low FPS. In Taki it goes smooth but sometimes it starts to slow down after around an hour of play. Pretty random, but as I said in Chernarus it happens quite often at the begining. The strange thing is that my brother has a lower end system (Core2Duo E6300, 4GB RAM, nVidia 9800GT) and never have this kind of slow down, neither do I in SP.
I play only Domination missions in MP.
My system:
AMD PhenomII X4 955 @3.6GHz per core.
Kingston ValueRAM 8GB DDR3
MB Gygabyte MA770T-UD3
AMD Radeon HD6850