OK, so looks like changing 802.11r to Adaptive has fixed it. We didnt have any issues with it set to enabled with Gateway APs, only on mesh repeater APs. The main reason we had it set to enabled rather than Adaptive was because Adaptive is only supported on iPhone 6s and above (https://support.apple.com/en-gb/HT202628), we have several iPhone 6 devices in our environment, which can now no longer make use of this roaming feature. But at least they are now able to connect. Not sure if this is a side effect of 802.11r enabled mode or a bug with Meraki.
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