Sounds like BBMD adjustments may need to be reviewed
Since there is a router involved, "2.1" and 1.1" (octets), review you BBMD's
to make sure they are set up correctly.
Additionally, I would suggest you take a hard look at the BACnet "BIBBS" and "Pics" for the different products on your site to see what limitations each has. My guess is you have at least a BBMD issue, and a secondary issues of some of the BACnet controllers not being 2008 BACnet compliant.
If any of your BACnet products are using BTL certified 135 2008 version compliance, then you will more than likely have to put in the BACnet MSTP network number into the appropriate control modules. Any of the BACnet controllers that are not BACnet 135 2008 complieant, may not bind to the newer BACnet devices.
Food for thought