What happened is that url protocols became case insensitive. So if you had added file: as a url protocol, previously it would trigger only on file:foo not File:foo. The solution is to change your entry in $wgUrlProtocols so that it is 'file://' instead of 'file:'.
--bawolff
Thank you bawolff. That explains the root of the issue much better as opposed to the change I needed to make to fix it, which would have been much more useful had I decided to keep File protocol links enabled.
I've opted to just disable file protocol links in general though as it was just a left over configuration change from some time ago that I had forgotten to remove when we determined we wouldn't be using it.
I think that's now twice in as many days I've been ninja'd in an email. Makes me laugh a little bit every time it happens.
Thank you, Derric Atzrott