ISP's actually have access to any data that passes the lines, for this reason its very unlikely that they would use this type of technology to monitor you, so its more likely that you have a virus or trojan that keeps reactivating itself. This is very common activity for trojans and spyware so the tick is to delete the file that is causing it all to reinstate itself. Often running scans in safemode will help in this and there are also other things to probably find out about that spyware try googling a bit more to get more info about it and specifially how to remove it (beware of anything wanting to sell you software to remove it however).
That said the ISPs do use software to auto detect certain p2p protocols and WinMX transfers happen to be an easy target for this software and this is what is used to slow those connection down when thorttling occurs or blocking. If you are on an ISP that does this there are not too many choices in fixing this except to move to an ISP that doesnt do it, or whose practices are ones you can live with. You'll be hard pressed to find an ISP that isnt doing this but they do exist so more research is in order for your area.
Hope this helps