I had a similar problem some time ago with one of the earlier Cubase 7 versions, and none of my controllers worked. Tried everything to no avail. Then Windows loaded some updates, restarted and everything was working fine. Since then, I've never experienced the same issue again. So, by all means, the first thing to try is a good ol' reboot.
Desktop: i7 3770k, 32 GB RAM, nVidia GTX770 + GT640-DCSL fanless, 3 monitors (30" 2560x1600 + 2x 27" 1920x1080), 256 GB SSD (OS), 2 TB SATA III (audio), 3 TB SATA III (sample libraries), 3x 3 TB USB 3.0 (backup/archives), RME UFX, Win 8.1 Pro x64, Cubase 7.5, Sonar X3, Vienna Ensemble Pro 5.
Slaves: 2x i7 2700k, 16 GB RAM, 256 GB SSD, 3 TB SATA III, Win 8.1 Pro x64, Vienna Ensemble Pro 5.
Laptop: 17" HP EliteBook 8770w (i7 3820QM 2.7 Ghz/3.7 Ghz max OC, 16 GB RAM, 256 GB SSD, 1 TB SATA III), RME Babyface, Win 7 Pro x64, Vienna Ensemble Pro 5, Cubase 7.5, Sonar X3.