My 2003 getaway "coolers" have always filled with water, especially after a capsize. Hobie has posted technical bulliten for this problem... loosening the side screws and tightening the middle ones...but it does not work.
http://static.hobiecat.com/2010_archive/support/pdfs/gwhatchleak.pdf
The lids simply don't ever seat completely against the rubber gasket. You could always try adding some other type of gasket seal, but it really is not worth it. Anything you are going to bring on a Hobie is going to get wet anyway! Invest in a small drybag for criticcals like cell phones or FRS two-ways...
I am not sure what the writers below mean when they refer to the drain plugs - my "coolers" don't have any drains. They do have inspection ports that go into the hulls, but if you remove these, you will end up flooding your pontoons....so leave them screwed on!!
As far as the mast squeaking...I had the same problem and tried a couple different sprays, i.e. sail-kote and a dry silicone spray...this lasted for a couple weeks, but the squeak came back. So I decided to try a Hobie teflon disk, although I did not think this was needed for this boat due to the delrin mast ball, but i figured it couldn't hurt. Problem solved...the boat has been silent all summer.
Happy sailing....