I've also found another interesting reason for not being unable to dry-dock--blackrock.
I've been dumping it on the deck of my ship as I mine and soon realized that it doesn't decay. I've had pieces sitting on my deck for over a week before I finally cleaned it up in order to dry-dock. Some of the pieces will land in weird spots on the ships and are very hard to pick up, let alone see without using context handles. While this can be used for handy storage of something that doesn't stack, if you sail around pieces of it will occasionally fall off the deck and will become jetsam in your wake.