Current BSAs: Bravil Docks, Complement, Meshes, QTP3 for B&M, Shipyard, Sounds EV, Textures EV, Textures.
I tried a clean test character as you suggested, and it worked fine. So, I suppose it's a matter of going down the list and seeing what the conflict is. An interesting note, the upper half of the city walls themselves are red-brick while the lower halves are a lighter gray. Also, some of the steps are of the normal grayish wood, and the others are darker.
You should be seeing most or all of Bravil with the vanilla textures when using those BSAs (vanilla but enhanced by QTP3) as the QTP3 patch for B&M (the one created by dev_akm) reverts the darkened B&M textures to the standard lighter ones, and thus our QTP3 for B&M BSA maintains that. If you want Bravil to appear dark like was intended with B&M, then don't use the QTP3 patch for B&M and don't use our BSA for QTP3 B&M.
Also, don't use "Better Cities - Bravil Docks.bsa" with B&M. You haven't followed the installation instructions we provided in the readme have you?

Please read the installation instructions carefully, it explains which order to install the files in, and which BSA files you should be using, and how many BC BSAs you should have after a successful installation.
Ultimately:
If you want Bravil to look like B&M intends, you should have "Better Cities - B&M.bsa" installed (plus the contents of the Meshes folder which comes with this BSA).
If you want Bravil to look more like it does without B&M, and you are using QTP3, then you should have dev_akm's QTP3 for B&M patch, and you should have "Better Cities - QTP3 for B&M.bsa" installed (plus the contents of the Meshes folder which comes with this BSA).
If you aren't using B&M, you should have "Better Cities - Bravil Docks.bsa" installed.
You should NEVER have more than one of any of these three BSAs.