I understand your dilemma. The trade off between the value of comments versus folks who have semi-colons in column one has to be considered. How about a comment character selection as part of the interface? I.e. default it to semi-colon or percent sign in first column ( or even anywhere ) and allow the user to specify.
--hsm
"Never try to teach a pig to sing...it wastes your time and it annoys the pig."