Hmm, maybe I was being a bit daft there - the rear fan has 2 connectors, an open one to the PSU and a small one (a single wire with a connector about a centimetre wide), the same as the one from the front fan, which fits the controller on the mobo which matches the one for the CPU fan. I had both of them connected, but swapping the small one for the one from the front fan seems to have done the trick.
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