As mentioned in this answer, since Git 1.8.2 you can use core.commentchar config value to change commit message comments to something else than the default #<
You should try to run :verbose syntax. The active syntax file is probably $VIMRUNTIME\syntax\gitcommit.vim (github version which is likely in your .vim).
It will tell you which syntax line will trigger the formatting as comment.
You'll probably see something like :
gitcommitComment xxx match /^#.*/
links to Comment
or
syn match gitcommitComment "^#.*"
meaning it matches every line starting by #.
You might be able to modify it so that a # on the first line is not considered as a comment. I don't know syntax format enough to give you a full solution.
\%^ match the beginning of file
\%1l match line 1
\%>1l match below line 1
So you might try to modify the gitComment pattern so that it does not work on line 1 of your git commit.
(I tried some things but did not manage to only exclude first line of comment ! It seems there is also a diffComment messing things up because gitcommit includes diff format with syn include @gitcommitDiff syntax/diff.vim)
)
For more details, see :help syntax and :help pattern.
Another good resource on syntax highligthing : Learn Vim the Hard Way, chapter 46.