It appears the themer version of the Jellybeans theme is only setting foreground colors in the sign column? The problem is that they are hard to see. Jellybeans uses both foreground and background colors.
" sets the highlighting for the given group
fun! s:X(group, fg, bg, attr, lcfg, lcbg)
"...
call s:X("DiffAdd","D2EBBE","437019","","White","DarkGreen")
call s:X("DiffDelete","40000A","700009","","DarkRed","DarkRed")
call s:X("DiffChange","","2B5B77","","White","DarkBlue")
call s:X("DiffText","8fbfdc","000000","reverse","Yellow","")
-- https://github.com/nanotech/jellybeans.vim/blob/ef83bf4dc8b3eacffc97bf5c96ab2581b415c9fa/colors/jellybeans.vim#L522-L525
It appears the themer version of the Jellybeans theme is only setting foreground colors in the sign column? The problem is that they are hard to see. Jellybeans uses both foreground and background colors.
-- https://github.com/nanotech/jellybeans.vim/blob/ef83bf4dc8b3eacffc97bf5c96ab2581b415c9fa/colors/jellybeans.vim#L522-L525