I'll leave it to people who've got more complete information, but for now, I'm pretty sure that the flotation foam does not even come close to half the hull volume.
One hull probably filled faster than the other because of any of a hundred reasons - most likely the plug was partially pushed into the dryer hull by the inrush of water, while not on the other.
Since you generally have a dry boat, just leave the plugs out while you store it to finish drying it out.
Now as for the hull being soft all over, that is probably a different issue - delamination. It's a well documented problem in this forum. for starters, look here
http://www.hobiecat.com/community/viewtopic.php?t=1156