I've not seen that, but it has been a while since I did RFB. Collision avoidance??
When you set the vessels to "Docked", are you also setting the speed to "0" (zero)? Also, the "Delete on last waypoint" should always be unchecked when the "Docked Ship" is ticked on. Have you looked under the vessels to make sure there is plenty of clearance beneath their hulls? Make certain that you have US fishing boats there. Do the Type= and Class= lines in the Sea and Roster CFG files match what the Campaign MIS files have?...
I've gotten your update, and we'll attempt to incorporate some of this into FotRSU. It might not make this next beta version, but we'll get it translated eventually.