
Smuggler Joe, and welcome aboard! Pull up a keg, have a seat, and have a couple on us!
This is a known bug, your rep problem... It's happened to a lot of us for no apparent reason. I think there has been some work to try to seek out the source of the problem but so far there has been no solution.
Best idea for gaining your rep back - go into the jungle and find a reload portal (reloads one area to another) near where some rapers are being spawned. Save the girl, go through the portal and back again, and if you continue to do this, more rapers will spawn and you can save the girl again and again until your rep is back up to normal.
This takes a bit of time and patience but it's cheaper (and makes you money!) than the church, at which I am told MAY take up to 5MIL to fix your rep... (yeesh!)
Did you ever get the officer problem solved? That could be a corrupted save, happens...
Try hitting the "T" button before you board your ship - that may clean some things up.
Hope this helps!

Again, welcome aboard, and I hope we see you in these fair waters often! :gday