I finally (after a bit of searching and thinking) figured how to properly match comments with flex/bison. Horray :)

Some tutorials use this in flex:

#.*$

But since flex chooses longest-match-first for the next token, any line with a # in it might have the remainder of the line accidentally cut as a comment. The right way to do this appears to be:

/* in your .lex file */

%x LEX_COMMENT

%%

"#" { BEGIN(LEX_COMMENT); }
<LEX_COMMENT>[^\n]*  /* ignore comments. */
<LEX_COMMENT>\n   { yylineno++; BEGIN(INITIAL); } /* end comment */

There's a mini state-machine going on here. When it matches a "#" it moves into the 'LEX_COMMENT' (name chosen by me, could be anything) state where only tokens in this state are accepted. Now my config files can ignore comments properly: only when outside the presence of any other token (like a quoted string).

Details here