The fuses don't have to be blown to prevent starting
SimkaXP, did you ever get to the bottom of your problem of beeps and sometimes no beeps?
I had a similar problem, though not identical with my '07 RXT. I was returning to the boat ramp after about two hours of riding and wave jumping without any problems at all. I got to about 100m from the boat ramp and the engine cut out and I couldn't start it again. With the current quickly taking me towards rocks, I flagged down the first passing boat. In the haste to tow me away from the looming rocks, he ended up turning me and the ski upsidedown and then left me stranded on the beach behind a rock wall. I couldn't get the RXT past the rocks (by swimming with it), so I walked to the NSW Maritime office (luckily it was less than half a mile) and asked for a tow. Sorry, it's a long story.....
Anyhow, after getting towed back to the boat ramp by the Maritime, I got the RXT home and no-load tested the battery with a multimeter, a bit less than 13V, so I tried to jump start it using my car battery (strictly following the instructions in this forum) and no luck. Every time I attached the DESS key, I got no beeps and the gauges faded away within 3 to 5 seconds. Just for kicks and because I couldn't find an exact match in the forum for my symptoms, I tried my (coincidently new) car battery instead of the RXT's battery and still couldn't start it or get any beeps. Sometimes I'd get the beep, beep, beep you normally get when you leave the DESS in. But whenever I pushed the start button - nothing, no cranking, nothing.
I checked all the fuses. The MPEM fuses were all fine, as were the main 30A fuses, none of them were blown. However, and this is the part that anyone with an electrical problem might find instructive, even if the fuses aren't blown, they still might be the cause of the problem.
How? Well, in my case there was a small amount of surface corrosion on one leg of the each of the two main 30A fuses marked as "charge" and "batt" on the fuse cover. I scraped the white corrosion (not salt, the fuse covers were working perfectly) off with my fingernail and re-inserted the fuses. Well what do you know - problem fixed.
The RXT is back to normal, beeps twice when you plug in the DESS key and starts when you press the start/stop button.
Again, I apologise for the long story, but it's such a simple fix (though it took me two days to find), I hope someone out there finds it useful.