well if I shut down my mule, its gone...sure you have not started it twice or soemthing alike?
are you running amule or amuled ? is it maybe the amuleweb which is running?
btw if you kill the process, this will not hurt your file system in any way, the only thing it could hurt is the files currently downloaded, but if they get corrupted, amule will simple rehash them at startup. so not a big deal
stefanero