I uninstalled qTranslate and all other plugins when testing this. I had never installed qTranslate Slug (though I might now - sounds interesting).
What I've now determined is this:
I was calling custom post types into the page and both the page slug and the custom post type slug were the same (I was attempting to use the custom post type slug argument to build a specific url structure). I can see how doing it this way would confuse things, but of course it worked fine in 3.4.0 so I didn't really look for another way of doing this. The fact that you can access the page with the uppercase slug is still a bit odd, however - not sure why that even works!
My new solution is to use parent pages within the custom post types to create my url structures, which was probably the right way to do it in the first place, but live and learn.
Sadly, I've used the other technique on more than one site, so I've got to rebuild things before my clients start updating!
Thanks for replying though!