Re: alt, shift, 3 not working
 

Something seems broken in how PT reads the Num Pad:
go to Keyboard Shortcuts
Activate "Search by Key"
Press Shift + some Num Pad keys
Result: keys 1, 2, 3, 4, 6, 7, 8, 9, 0 and "Comma" are not recognized as Num Pad keys but standard cursor keys instead.
If you use other modifiers (Ctrl, Alt, Start) _without_ Shift (or no modifier) all the Num Pad keys are recognized properly.
(Tested on Windows)

So Alt + Shift + NP 3 is recognized as Alt + Shift + Page Down (and can be set as the shortcut for Consolidate Clip as a dirty workaround)

Re: alt, shift, 3 not working
 

NumPad on Classic or Transport in Operations tab in preferences? This was reset for me recently in an update. I wanted Classic, but it was default to Transport. Does yours say Transport? Does Classic make the behavior what you expect?

Re: alt, shift, 3 not working
 

The key reported by Search by Key is wrong in both Classic and Transport modes
I reported this Shift + Num Pad behavior as a bug, hope for a fix