Thank you both Xenonsurf and Sailor Steve for your input. I haven't attacked ships in port as of yet and won't based on your feedback. I suspect the problem may be that I have "Indian Ocean Campaign files only" activated in JSGME. If I want to do the Indian Ocean campaign when should I activate that mod?
I don't know why the "NULL" grid patrol option is occuring or why I cannot change it in SH3 Commander. However, I found something of a fix by simply docking immediately after mission loads. It costs me a patrol but fixes that problem. Oh and I always set SH3 Commander to automatically roll back.