That makes sense. However, if I recall correctly this is happening not only for P2P. I'd understand that almost all ISP's have some kind of a traffic shaping for P2P traffic but this happens with usenet too which is very very rarely used here in the Philippines. They don't even know what it is.
I haven't tried using a VPN but that would be a good test. But in my initial traffic monitor graph, does that point to throttling even though those dips are only for a few seconds that I don't even see the drop in speed in the actual download clients themselves?