Yoav,
The cloud similarities do not look unexpected to me.
Remember SeaWiFS and MODIS view the same bits
of ocean within a few hours of each other. Clouds just
don't change that much over such a time scale. Granted,
over an 8-day period, many of the clouds will get filled
in, but areas with persistent clouds should still retain
the same relationship between SeaWiFS and MODIS.
I'm attaching a SeaWIFS/Aqua-MODIS comparison
image for the 8-day period you named just to make
sure we are talking about the same thing.