Weird. You've tried pairing each remote with a single device, and also tried disabling IR on the MBP which would be my other suggestion.
Did you do the pairing one device at a time with the other swicthed off?
Apart from rebooting and repeating the steps or a poor suggestion of obscuring the IR sensor on the MBP if you can locate it I'm not sure what you could try next.
Which version of Mac OS is on the MBP - check if other users have remote issues in case there's a bug in your software version.
NOTE - Ensure you only follow the instructions for your SPECIFIC Mac model family and not not try things designed for older Macs on newer ones. If in doubt don't do it.
Links below have related links at the sides which may be more applicable depening on OS and model.
I've tried reseting the SMC, PRAM and repairing permissions to no avail.
I'm running Lion 10.7.2.
I've tried using the same remote on another laptop and toggling the disable remote IR checkbox kicks in immediately.
I'm going to get an iMac any day now so will just park this until then.
Thanks for your help!