I had the same problem with a 4.3 190 horse/alpha drive motor in my previous Glastron SX190.  
87 octane:  When shut down after pulling tubes or working hard, the motor would diesel for a while.  Very annoying.  Let engine idle for 2-3 full minutes before shut down, then it usually didn't diesel much or at all.
89 octane:  Same as above, but the engine would diesel for a few seconds after working hard.  Let idle for one minute to cool off, and then would shut down OK.  
93 octane:  I could run the engine and shut it down without any issues.   
I chalked it up to a very close tolerance timing and compression setup, where Merc was trying to get the best gas mileage and least amount of emissions from the engine.  Wound pretty tight.  I didn't want to retard the timing, so I burned the better octane.  The people I sold the boat to run 89 octane and let the engine idle for one minute before shutting it down.
					
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Previous Four Winns:  2003 Freedom 180, 150 Johnson XL, purchased new July 2005, sold Sept. 07
Current Four Winns:  2002 Horizon 170, 115 Yamaha V4, purchased May 2010 from family friend.
