From 1.9, setting a numpad number for controls gives identical ID as one on top of the keyboard, the distinction is lost. Say you have a numpad 1 set to drop items, now pressing it will switch to inventory slot 1 instead.
Tested with previous Minecraft versions and the issue seems to have only arisen from 1.9 - previously there was a distinction and keys were named differently. Please sort it out, it's very annoying. I'm hoping this won't be permanent... (If anything, we should have the choice if we want numpad numbers to allow switching to inventory slots or not).