I have the same problem on my 323 Doyle StackPack. My sail just went to the cleaners to deal with those splotches. So much water gathers in the sail and cover that I have to close the ports before hoisting the main. Learned THAT ONE the hard way. I snubbed up where the 'pack covers the mast, but apparently the water trickles in the top zipper of the 'pack. The flap does not keep the water from running under it. I believe that the bimini prevents the boom from being at a low-enough angle to let the water run out. I have the 'pack here at home to put some drainage grommets along the lower edge.
My first thought was a "curb" parrallel to the zipper, under the flap, would direct the water aft on the 'pack. Maybe velcro. but that is a pain in the aft of it's own. Maybe a strip of sewn-in webbing MIGHT suffice. Or a bead of silicone sealant left to harden for a curb would do, but I don't know if that would stick to the fabric. I found "awning rope" on page 157 of the Sailrite catalog. It's like a boltrope on a sail. It is a 3/8 inch tube with a sewing lab. $.75 to $1.75 a foot. There is a Sailrite store here in Annapolis. As soon as I get my buddy's bimini off the sewing table I'll do the StackPack sewing, but it won't be until I get the sail back at the end of February and put it all on the boom will I know if the problem is solved.