it has been so long since i dealt with this i don't know if this helps but i think when you have a batch file such as startup_sequence it opens a shell while working. as long as the program started by this batch file is running that shell won't close. well unless the output is sent to >nil or >null. so chances are those shell processes are being held open by a certain process.
dangit i got bea by two people. i suck at typing.