Mine sits inside or on a covered lift so I don't normally get the "streaks", but the times that it has been in the rain I've gotten them. I always thought it was dust / dirt and maybe dye coming from the canvas, the rain "washes" it out and it runs down the sides.
It washes off, or if you have a good coat of wax, it wipes right off.
I think the only way to prevent it is to get a full cover that goes to the rub rail.
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05' Chaparral 220 SSI
350 Mag / B3
Seadoo GTS