I'm guessing this is probably a savegame compatibility issue? Many CoA are blank, appearing as solid black. The effect seems to be grouped roughly by de jure kingdoms and likely religion is playing a role. At least in part it seems to be a matter of religious mismatch with the de jure title though I'm not sure against what standard. For instance in the screenshot Mauretania's CoA is fine but all duchy and count CoAs under it are black. Algeirs meanwhile has the Kingdom CoA black also. You can also see how Wales is affected from Kingdom down to county level.
The affected areas are Scotland and Wales, all of Africa (the Muslim emirates and shiekdoms in Egypt and Ifat are not affected). All Christian titles east of the Bosphorus, and south of the Caucuses (Georgia is affected, Azov and Alania are not, crusader Syria and Jerusalem are affected, de jure emirates that are Muslim are not). Farther east Zoroastrian Khwarizm is affected but it's Shia vassals are not. Orthodox and Tengri counties vassalized to Ilkhanate are black where they are de jure in Khwarizm but normal elsewhere. Unheld duke level titles of the kingdom are black while those held by Shia or Hindu characters are normal. No Muslim or Dharmic held titles are affected.
If uploading a savegame helps let me know and I'll do so.
EDIT: Forgot important info:
On Windows 8, through Steam, all DLC except Aztecs, no other mods, checksum EDDG is current.