If there isn't an explicit vlan mapping in the FlexConnect group then the WLAN will map to the VLAN specified under the WLAN config. However if VLAN support is not enabled for the FlexConnect group then traffic tagging is not supported and so the traffic will be dropped off on the native VLAN of the AP.
Also check if the WLAN are centrally or locally switched. If centrally then the VLAN config on the Flex group is not required and the controller will deal with the tagging.