Not the answer to your specific question, but here are some useful settings that may help.
"" Diff options; ignore whitespace.
set diffopt+=iwhite
I don't like: diffon: diffoff, because they fight with word wrap (turns it on when you exit diff). Therefore, I install only diff, scrollbind, foldmarker and foldcolumn.
"" Diff 'd' {{{
nmap <silent> ,dd :set diff scb fdm=diff fdc=2<CR>
nmap <silent> ,dD :windo :set diff scb fdm=diff fdc=2<CR>
nmap <silent> ,do :set nodiff noscb fdm=manual fdc=0<CR>
nmap <silent> ,dO :windo :set nodiff noscb fdm=manual fdc=0<CR>
"nmap <silent> ,dd :diffthis<CR>
"nmap <silent> ,dD :windo :diffthis<CR>
"nmap <silent> ,do :diffoff<CR>
"nmap <silent> ,dO :windo :diffoff<CR>
nmap <silent> ,du :diffupdate<CR>
"" }}}
, DirDiff , ...