Is there a specific reason that git gui does not respect comment lines added by a git hook?

Hello,

I've written a prepare-commit-msg hook that maps Team Foundation Server workitem ID's to a Git commit message. (When committing, a picklist appears. Users can select one or more workitems and the workitems are added to the commit message using a specific format. Later on, we use git log --grep to search for specific commits belonging to a workitem).

I'm using comments in the commit message to give additional information to the user. For example, when the Team Foundation Server is not available, I add the following comment to the top of the commit message.

# Warning: could not access Team Foundation Server at <servername>. Check your configuration or manually enter your workitem.

Because the line starts with a # sign, it is not added to the actual commit message...when using git commit. If I use git gui, the above comment appears in the git gui interface but *is* actually added to the git commit message when committing.

Is there a specific reason that git gui is actually adding lines starting with a # sign? I was expecting it to ignore those lines.