That is the strange thing, the engine running or not shouldn't make any difference. The op's car knows the handbrake is on so let's the roof work, but as soon as the engine is running. It decides 'I'm not having any of that and doesn't allow the roof to work.
I think I would try another roof module and see if that makes any difference.
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2001 V40 2.0lt Sport lux - Daily Driver. 174k miles.
2003 C70 2.4 GT Convertible - Garage Queen. 65k miles.
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