I've just found this question as we had the same issue. The underlying problem is that both boards will assign the same MAC (BSSID) for the AP interface on wlan1. The MAC needs to be unique per channel, just as it does for ethernet per LAN segment.
You can change the MAC for wlan1 by setting wlan2addr in U-Boot environment. Not wlan1addr as one might expect, that would be used for an ad hoc/P2P interface. If you don't do this, then you will still have trouble if Auto Channel Selection gives the same channel number to two devices.
Any kudos here is really due to Digi support for the very rapid response, thanks guys !