The CC updater is a little bit erratic still. On one of my two systems I have the same as you, Photoshop doesn't see updates and just reports "up to date" through CC. But if I go through Help > Updates it works, so I use that.
The official solution for this is a full uninstall/reinstall of the "offending" app, with the explanation that the updater "doesn't recognize" the application because some files are missing. I might have considered that if Help > Updates didn't work either, especially since this is now the only way to get updates.
Anyway, the version mismatch isn't all that important as long as the major versions are the same. If they aren't, there is always the option to "Render Using Lightroom", which works just as well, you just lose some flexibility such as opening as smart object/layers/HDR.