Consider this less of a tech support issue and more of a public service annoucement ...
With 5.0.4, I figured it was time to muck out the stables, so to speak, so I threw out all my addons and turned the hose on my WTF file.
When I logged into the game, I noticed things were a little out of whack. The nUI modules at the bottom of the screen all fit like they normally did. But everything else -- my bags, the mailbox, the game menus, the box you get when you hover your mouse over another character or NPC -- were small. Really, really small.
I'm an old guy, and the scale my game defaulted to was just too darned small. There's no simple option to adjust the nUI scale, I fiddled and tinkered and finally found a note from Scott buried in an old forum somewhere that solved my issue. I'll paraphrase it here.
1. Go to the in-game Video options screen. Go to the Advanced settings.
2. See the UI slider? Check the box and then use the slider to set things (i.e. the Blizzard stuff) like you want. Ignore the nUI components, which will swell or shrink.
3 Reload nUI (either /reload ui or /rl nui should work). nUI will fit itself to the screen. Done!
Hope that helps someone else in this post-patch/pre-Mists era.
Love nUI. Can't wait to see what 6.0 has in store.