In that case I think it has nothing to do with docking at the tanker. The bug where no tonnage is credited after a patrol has been around for ages. As far as I know there is no sollution for this. One advice that's usually given, is not to upgrade the boat before first patrol. What I usually do, is to save right before docking and load the savegame if the bug occurs, more often than not the tonnage is credited after reloading.
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