Most tooltips in the topbar are capitalized:
But not the reputation:
Let's capitalize your reputation!
I think the rationale is the same as the footer copyright being lower case.
I'll quote the same sentence from Jeff:
It's not a complete sentence, so it doesn't need to be capitalized. We don't capitalize the tabs on the user page, or the homepage, for example
So, the words "your reputation" can't really be seen as "complete sentence" that stands on its own, hence should not be capitalized.