I use customized FreeRADIUS servers to handle authentication for Meraki in many locations.
If you haven't already tried, I suggest running FreeRADIUS in debug mode ( radiusd -X ) and attempting to connect to your SSID. You will have to look through the FreeRADIUS output, but it should provide an indication of the root cause.
Are you using Meraki's RADIUS proxy?
Have you configured FreeRADIUS to accept connections from all possible IP addresses that can originate the RADIUS requests? The IP ranges will be different if you use Meraki's RADIUS proxy.
If you aren't using Meraki's RADIUS proxy, have you checked firewall configurations between your access points and your RADIUS server?