I have had the same issue for about 8 months now. When I put the top up and latch it, it might start beeping. Other times it will start after I hit a bump while driving. The mechanic diagnosed it as the sensor in the drivers side header. Next it was the guides being worn. Because it does not do this all the time, fixes seem to have worked for a while but no cure yet.
I had noticed that after I put the top up and it beeps, when I unlock it, the hydraulic cylinders seemed to have backed off a bit and I have to run the top up cycle for a couple secounds then it is ok. I believe the fluid is leaking and allowing the tension in the cylinder to relese.
A couple weeks ago the system started making a really bad whining / screeching sound and stopped working. The mechanic determined it was out of fluid, so they filled it and it worked, but they couldn't find a leak. The day after I picked it up, the beeping ocurred and the screeching is coming back. I am positive that the hydraulic system is the problem.