Keep in mind that the skimmer body itself isn't getting any larger. If you put the larger volume pump on it, you will be pushing more water through the skimmer...faster. I don't know what the perfect amount is, but I'm pretty sure there is a flow rate that is simply too much.
At that point, water/air would just be blasting through the skimmer with no time to interract with the air.
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400 gal reef. Established April, 2007. 3 Sequence Dart, RM12-4 skimmer, 2 x OM4Ways, Yellow Tang, Maroon Clown (pair), Blonde Naso Tang, Vlamingi Tang, Foxface Rabbit, Unicorn Tang, 2 Pakistani Butterflies and a few coral gobies
My Tank: http://www.canreef.com/vbulletin/showthread.php?t=28436
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