Thanks for your replies!
The problem occurs when the hood is down, and the misfit is towards the rear, where the clamshell/tonneau stands proud of the boot/trunk lid.
I suspect my drive cables are perhaps weak and twisty, as it seems to me that the motor lacks enough force to pull the clamshell down , squashing the hood down so everything is snug. I can press down on the clamshell and get a good fit, but it springs back up again about half an inch or so.
Nev
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