I have employed this method on both my boat and a friends boat and let me tell you it takes FOR EVER to drain the oil this way. I can't believe that this is an isolated situation because both of our boats do the same thing! I even pulled the motor and blew the hose out with a compressor. It was free and clear. My next idea is to open the drain hose and make a fitting to connect the compressor (throttled down of course) to the dipstick opening. Then again maybe I should just buy larger ID plumbing.. On the other - other hand, maybe I should just use a garbage bag with saw dust.
Were the engines warm before you drained the oil? It is not as fast as using a pump through the dipstick, but I have not had the problems you have had. I usually let my drives drain overnight though so maybe i am just patient.