This gave me something to think about, I have the oxide zipfile and mods saved in a common shared folder for two servers to access, this is where I place anything that has had an update. When the script starts it copies those files to the server folder, moves the mods to the oxide plugins folder, then unzips the oxide and over writes the older files, once done it starts the server. I've now seperated the update part and the server start in to two seperate scripts. I will see how that goes for a while.
Thanks Wulf for some idea what to try.