I updated from Krita 2.9.9 to 3.1.2 and the "zoom in" and "zoom out" keys on my Microsoft Wireless Keyboard 3000 stopped working. They are separate special keys on the left edge of the keyboard (see image) and they work properly in pretty much all other applications. Still in the previous version I could zoom canvas in and out with these keys.

But now if I try to register them as a key combinations in Canvas input settings, the zoom in key registers as "Shift" and zoom out as "Alt". I'm not sure if they were in this order or vice versa, I already uninstalled 3.1.2 and went back to old version. In 2.9.9 their key combinations were Ctrl + _ (zoom out) and Shift + Ctrl + = (zoom in).

These keys were very useful for me (because of my work ergonomics), and I really need them to work in future versions also

I'm running Windows 7 Home Premium with Wacom Intuos Pen

If you _really_ need them to work, you'll have to do some debugging yourself, because we don't have your hardware and anyway...

If Krita's shortcut dialog gets alt and shift then that's what the system (the driver, windows or the Qt development framework that Krita uses.) sends Krita. The big difference between 2.9 and 3.x is the version of Qt: we went from version 4 to version 5.

Krita doesn't listen to scancodes itself, it doesn't do low-level things like that. Krita gets key events from Qt, which gets key events from Windows. You could try with another Qt5-based application to see what that application gets -- if that's also alt and shift, then it's likely Qt.

Same bug here. Krita gets the SHIFT+ALT+LeftMouse shortcut for PAN Canvas when configuring, but it doesn't work when drawing. Win7 + Wacom Intuos 3 tablet.
Investigating for QT5 based apps.

(Config and use works with other commercial programs, like 3DSMax and Mudbox.)

SOLVED!

I stored a desired new SHIFT+ALT+LeftMouse shortcut for pan canvas (LMB = Wacom tablet pen tip in this case), which was conflicting with Canvas Input Settings ==>> Alternate Invocation's same settings there.

Solution:
I went to above Alternate Invocation and deleted the conflicting default shortcut. Voila! My beloved shortcut I use everywhere to navigate instantly works in Krita!! I'm ssoOooOoo happy now!! to the developers for amazing Krita!!