My 2006 roadster developed a terrible knocking and rattling noise which appeared to be on the left front behind the bulkhead? However,on a hunch, I drove with the top down and the house went completely! So, what causes this noise with the top up? I have checked that it is locked in place correctly and it seems fine?

 

Take that cover off and see if you have loose hardware in there. Once you get in there, you will see what I mean.

The other POSSIBLE problem is that the clamp that grabs the windshield frame on that side is not grabbing tightly enough and is "walking" and making noise as you drive - I can't remember exactly how the linkage is set up to compensate for this, it should be obvious when you get in there. It's a pretty simple mechanical setup that links the "D" handle to the clamps.

The service manual goes into fair detail about this, altho their stupid sketches are hard to read, why they couldn't provide photos as well is beyond me.