While a ship train is docked automatically (no redstone locking), every single chest barge only will be loaded with items in its first 6 slots, then the train undocks and travels on. Doesn't matter if the items are unstackable or not.
Paradoxically unloading items automatically will work with a full barge, just loading it fully doesn't work.
Is this intended behaviour or a bug?
Tested in v1.0.4.

This is a bug, will try to reproduce and fix

Bug reproduced, thanks a lot for reporting!
This was caused by default itemhandlers for mobs which have 6 slots for hands+armour. Since chest barge uses simple vanilla IInventory the default itemhandler managed to confuse the dock.