05 Roadster, have been manually raising and lowering the top due to hydraulic issues and a broken tonneau cable.
When the top is raised and the tonneau top latches using the manual tool it is locked, but the conv top switch blinks as if it is not. If I take the tool with the top in place and slip it onto the latch and apply just a little pressure the blinking light goes away…as long as you hold pressure on the tool. If you relax the pressure and remove the tool the blinking light returns.
Have you heard of this one before? Do you think the latch is failing?
No issues at all with bringing the top down and locking it…no blinking light.

 

I'm just guessing, but it sounds like a contact issue. Maybe a wear spot or dirt on the switch or latch mechanism is not letting it make full contact until you push it past that point with the tool.

 

Yea, that little switch is bad OR the lever on the switch is bent a little, such that the switch does not close during normal operation.
We are seeing more and more of this as our cars age. Try taking a look at the lever or "cam" that closes the switch.

Ive not dealt with this, so I can't say I have experience with it, but again, we are seeing more and more switch issues there, and in the "top open" and "retainer latch" switches.