Windows 7 SP1, Cubase 7.5.4, UR22 mkII, MIDI recording out of sync

As the subject says:

Windows 7 SP 1
Cubase 7.5.4
UR22 mkII with latest drivers for Windows 7.
Keyboard is NI S88 via USB, latest drivers.

I have used this exact same keyboard, with this exact same PC hardware (with Windows 7 SP1) without issues for years.

For some reason somewhere I upgraded Windows 7 to the latest service pack, but the only hardware change that was made was the UR22mkII. Since doing so, when I record MIDI, it plays back out of sync, in other words when I am recording I am hearing the click at a certain point, and I play in time to it, when I play back, the MIDI is visibly out of sync not only on playback but graphically in the midi editor. I wasn’t able to test my old interface with the software update to isolate the interface.

I tried ASIO4ALL and this seemed to fix it, but that is causing issues with the rest of the OS, forces me to restart every time, so not really a fix. What is causing this? Only thing I can think of is Steinberg USB driver.