Problem with line numbering in BMC Journal template

It should be their problem, not yours. However, you can accomplish the annoying editor's wish by adding the following magic to your document preamble:

\usepackage{etoolbox}
\makeatletter
\patchcmd\set@numberlines@box{\rlap}{\@gobble}{}{}
\makeatother

Where? I'd say just before the silly \def\includegraphic{} line.