I see there have been no responses to this question, but I have long wondered about this issue myself. I am using CS5 and have been looking for some kind of work-around that allows the alternating fills to begin with the first color each time it moves into a new column.
I also require a solution to this issue. Of course i could manually recolor the boxes at the cell-level, but given the volume of tables in my document, that would be very time consuming.
kind of tricky, because what you're asking goes against the alternative fills logic. Basically you ask to have two following lines with the same fill colour. By the way you can suggest this feature to Adobe developpers: an option to resart the first line of a split table with always the same colour. Anyone knows a script that would do that?