The ajh.vim colorscheme defines some theme colors by defining new syntax groups. Syntax elements are styled by linking to these elements, so to make Collemts gray italic for exmaple it does this:

hi GreyItalic      guifg=#626262 guibg=#1c1c1c ctermfg=241 ctermbg=234 gui=ITALIC
hi! link Comment GreyItalic

Unfortunately, this makes comments appear in the GreyItalic syntax group, which breaks any plugins that look at the group. YCM does this (to switch completions on/off in comments).