I'd suggest downloading Process Explorer from Sysinternals and looking at the different java.exe processes more closesly, that way you can get a better idea of which one to kill.
http://technet.microsoft.com/en-us/sysinternals/bb896653.aspx
It's very intuitive and you can find the java.exe processes and right click and goto their properties, from there you can see their command line, time of creation, etc which can help you find the process you want to kill.
Hope it helps.
