'Archives' and 'Game Files' from the ini:
[Archives]
Archive 0=Tribunal.bsa
Archive 1=Bloodmoon.bsa
Archive 2=Connary's BSA v2.bsa
[Game Files]
GameFile0=Bloodmoon.esm
GameFile1=Morrowind.esm
GameFile2=Tribunal.esm
I think i will try a fresh installation.
Since you have the BSA registered correctly, it's likely the problem lies in that your custom BSA contains assets which have the same names and path as the stock assets. You need to date your custom BSA earlier than the stock Morrowind BSAs so that the versions of the assets it contains will override the stock ones.
Files in the archive inherit the timestamp of the BSA, and Morrowind will only load the first instance of an archived asset based on timestamp.
Any assets not contained in your custom BSA will be taken from the stock archives.
[edit] also make sure that when you are redating the BSA that you change both the created and modified dates.