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I'd say that this is a security system issue and its quite possible that the ECU is at fault
I'd suggest to send it off to this firm
as they can test the ECU for all its function and confirm that the security features are correctly enabled
any replacement ECU has to be coded up to match the security present in the key and trasnmistter module so I'd say to get in touch with the firm I've already mentioned ( as they specialise in ROver ECU's )