i don't know how it works for sure on windows, but a similar situation exists on linux, where you get the pid of the bash shell, not the executable eventually being run by bash.... see Killing children's of children

...there are a few workarounds.... use killfam ( or the win32 version) to kill the pid and all it's children.....or you can spawn a command shell with ipc, and print the name of the executable you want to run to the shell's stdin.... probably something like the Win32::Job module is what you want....see Kill a process in Perl and killing on win32 and A killall for Windows