In older versions of the game, some keys were not usable in controls on certain layouts. MC-30704 addressed this issue, and now those keys can be selected as desired. However, in the inventory screen, those keys that were unselectable before still cannot be used to shift items directly into a hotbar slot.
Example: in my layout, the following keys occur where 1-9 appear on Qwerty: &[{(+=*)}. Despite mapping these keys to hotbar 1-9 in controls, and these keys working correctly to select the hotbar slot ingame, most cannot be used to quickly move items in the inventory screen.
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Confirmed for 15w49a.

Still an issue in 15w49b

Still doesn't works in 15w50a.

Also an issue in 1.8.9

an issue in 15w51b

This issue perfectly describes my problem (Ubuntu + Foreign Layout).
It is really annoying to me and I'd love it to be fixed so I can play properly again!
In the meantime I'll take any hotfix suggestion.

Still an issue in 16w02a.
I literally can't play the game with my current hardware because of this and so many other issues related to it.

Still an issue in 16w03a.

Still an issue in 16w06a.

Still issue in 16w07a

Also an issue in 16w07b

Confirmed for 1.9-pre1
I also saw something intresting, in the control seetings menu is the key that work written in text while the other ones (which don't work) are just the symbol of the key I'm pressing. You can see this here: https://i.imgur.com/K5sTieH.png
I'm using an azerty keyboard.

Still an issue in 1.9-pre3 and 1.9-pre4

I'm not clear on how this is a duplicate of MC-577.

MC-91315 should work.

Yup, that's fair.

This is still an issue in 1.12
To be specific : Pressing 2 or 6 while pressing shift has no effect
Still an issue in 15w46a, with the AZERTY layout on linux (Linux Monkey-Arch 4.2.5-1-ARCH #1 SMP PREEMPT Tue Oct 27 08:13:28 CET 2015 x86_64 GNU/Linux).