You have to enter the docks and after two in-game days have passed, provided you are in the Docks or when you re-enter them, WWMINSCINDOCKS will be set to 2. Leave the docks again and Minsc will immediately discover that Boo is missing provided that
i) no enemies are about
ii) the quest is triggered before Chapter 4.
If enemies are about, he should discover Boo is missing after the enemies are slain.
In the future, guys, try and post any problems in the support forum,
http://forums.pocketplane.net/index.php?board=19.0 . Not all of the mod team is registered here, including the author of the Minsc/Boo quest. Thanks!