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I had the same problem, I did:

au VimEnter * highlight clear SignColumn

Works like a charm, thanks :)

I had the same problem at first. Try putting it after wherever you're loading the plugin itself.

edit: Also, thanks airblade. I think I'm going to keep using this.

I experimented a bit more and found if I put it before my "syntax on" and color scheme setup lines it doesn't work, but if I put it after them the fix works. Raticide's comment clued me in.

You colour scheme is probably overriding it. You might want to edit your colour scheme's script and add it there.

Try

hi SignColumn ctermbg=232 guibg=#080808