Okay fixed it.
1. The Sub Category config file for BDB in 000_FilterExtensions_Configs was missing. Was able to copy that over from the Bluedog_DB > Compatability > Filter Extensions folder.
2. The names in the category list in each of these config files below need all need to match. That is, if you're not using the Real Names config patch, then they need to be the Kerbalized names (Sina, Kane, etc.). My issue was that the lists in each of these configs were different variations of the list itself and the names:
GameData > Bluedog_DB > Combatability > Filter Extensions > Mod_Bluedog Design Bureau AND SubCategories_BDB
Game Data > 000_FilterExtensions_Configs > SubCategories_BDB (This was completely missing for me. I had to copy and paste from the Bluedog folder.)
Game Date > 000_FilterExtensions_Configs > Default > Mod_Bluedog Design Bureau
3. This is the correct list of subcategories with Kerbalized names. Copy and paste this into each instance it shows up in the above config files:
SUBCATEGORIES
{
list = 0,Pods
list = 1,Fuel Tanks
list = 2,Engines
list = 3,Command and Control
list = 4,Structural
list = 5,Coupling
list = 6,Payload
list = 7,Aerodynamics
list = 8,Ground
list = 9,Thermal
list = 10,Electrical
list = 11,Communications
list = 12,Science
list = 13,Utility
list = 14,Viklun/Etoh/Chryslus
list = 15,Prometheus/Konan
list = 16,Bossart/Muo
list = 17,Fenris/Daleth
list = 18,Sarnus
list = 19,Belle
list = 20,Inon/Vejur
list = 21,Hermes/Leo
list = 22,Kane
list = 23,Sina
list = 24,Probes
list = 25,Hokulani
list = 26,Solid Stages/SRBs
// list = 27,unsorted
list = 99,Undefined
}
}