With the inline six firing order (1-5-3-6-2-4-1-5-etc.)cylinders 1 and 6 each follow 2 and 5, respectively, by only 240 degrees. Cylinders 3 and 4 are "evenly" spaced at 360 degrees. With a typical high-performance cam the intake valve on #1 (or #6) will start opening while #2 (or #5) is closing. This will certainly affect the flow into 1 and 6, both from a flow momentum and wave dynamics perspective. It is not surprising that dividing the ports or using asymmetrical valve timing would affect or help a six with siamesed ports.
