If it feels like you're skipping but nothing is amiss, then it is possible you could be sucking air. This happens to me when in moderate chop or trying to ride boat wakes, when the fins can grab a little air; but not on smooth water.
Mine doesn't make any inappropriate noises though either, so I'm wondering if your chain is snapping against the sprocket edge. Do you have the old style drive (stainless sprocket)? Just for drills, it might be a good idea to inspect your chain tension and drive shaft bushings (older style drive only), and lube your moving parts (including the chain) to see if it makes a difference.
The following settings work well for me: the front chain should have no more
than 1/4 " give
per side (with a good squeeze) -- 3/16 is better; the rear chain is good with about 1/8"; the idler pulley cable should also have about 1/8" squeezable give
per side. Less than these and you start picking up added friction; more and it gets a little sloppy and more vulnerable to chain skips. The tightening procedure should be in your Hobie manual (also available on line if you don't have one).
As a final thought, make sure your drive is well secured in its well so it's not moving around.