Chris, I and many others have exactly the same problem.
Like you, "obvious" causes have been eliminated eg Batteries, Interference from CFLs etc, but it just persists.
I'm sorry to say that the consensus is that the cause has not been pinpointed.
We control a TV, a DVD player and a HiFi system from our Foxsat Telecommander and have, through exhaustive experimentation, found that it absolutely does not relate to directionality, for example: ie Provided one notes that device selection is acknowledged by a flash of the relevant Red LED we can wave the Control in any random direction and subsequent commands are acted upon.
But in HDR mode, things relating to Live Pause,and many other features just take ages to respond.
It is an as yet unresolved conundrum.- We've tried Factory Reset, we've upgraded to the Raydon Customised Firmware and we've otherwise exhausted the box of tricks. Yet the issue remains.
We have, therefore, simply adapted and learned to live with it. There will be no more Upgrades, so .............
PS: I don't think it's a Hardware issue, so please don't prise open your Remote - you'll just get bits of plastic spraying around the carpet and might get angry!