In update to my post above, I contacted my rep who agreed it was ridiculous and got in touch with Experian to get the discrepancies removed... Came back frustrated when he got the same response from them as I did
I had no choice but to remove the AT check, he did say they are taking all feedback on board and a lot of dealers are having the same issues so it might get tweaked in the future.
The car that was showing a discrepancy was getting a lot of interest before they introduced the check, not a single enquiry since the car was flagging up as a discrepancy on the advert and since I've had the AT check removed, I've now taken a deposit on the car.
I'm trying out motorcheck.co.uk for HPIs at the moment, £3 for a hpi check and they also have spec check. Well worth a look.