You definitely want to consider calling TAC to verify your configuration. At first glance, this looks like you are running into the known collision between route-based VPN and domain-based VPN (VPN encryption domain groups). To work around this, you can define VPN domains-per-community for each gateway. Be sure you have an empty object group (yep, a group with zero objects in it). Edit the community, select the center and start gateways, then edit the VPN domain on each gateway to use the empty group object.
I'd also suggest unchecking "allow all encrypted traffic" in the community. This could lead to these sorts of unintended consequences, but you can try with/without it.
Typically, for route-based VPNs, you need to use VPN Directional match in the rules. You first need to enable directional match in Global Properties - VPN - Advanced. In a given VPN rule for those gateways, edit the VPN column, and choose "Directional match" option, and create three separate entries:
internal_clear -> <community name>
<community name> -> internal_clear
<community name> -> <community name>
You said you have BGP between VPN peers, so I presume you have VTIs configured and operational. You will want to review your route-maps to make sure you are dong AS PATH filtering, possibly pre-pending, to make sure you don't have one gateway end up being an inadvertent hub (unless you want that; but then you have to edit your VPN directional match rules to allow traffic to flow correctly).
Good luck!