I have a similar problem. My 2005 Waverunner FX HO will not transition between locked and unlocked. When it is locked, you can lock it over and over again and the security functions as expected (beeps once and disables start button). When it is unlocked, you can press unlock over and over and it functions as expected (2 beeps and start button works). When you try to transition between the locked and unlocked (or vise versa), the security seems to freeze up and it will not start, beep, or anything. The only way to get it to transition between locked and unlocked seems to be to disconnect the battery for a few minutes, reconnect it, and then change the security mode.
Michael, October 2009
