Minecraft Version: 1.7.10
Inventory Tweaks Version: 1.59-dev-152-cf6e263

When auto-refill kicks in with certain items, such as multiple types of Chiseled cobblestone, when a stack runs out it will grab any of those kinds no matter what other's of the same kind you have. This is a fairly annoying issue when working on something like a big reactor and you have multiple of the blocks in your inventory, you run out of a stack of casing, instead of the second stack of casing it will grab something like an exhaust port. I haven't tested it, but I think this may also happen with different kinds of wool or stone bricks.

Minecraft Version: 1.10.2
Inventory Tweaks Version: 1.61-58

I'm having this same issue with Vanilla stained-glass.

1. I have an inventory full of blue, green & red stained-glass, playing MC while watching TV.
2. I'm looking down, holding Ctrl, walking and placing Blue stained-glass ( absentmindedly ).
3. The stack runs out, auto-refill kicks in and BOOM I'm placing Green stained-glass.
4. When I finally realise, I have to back track, remove the Green and enter my inventory to grab the Blue.

I'm currently working on a very large glass structure and this is becoming increasingly frustrating...

It might be nice to have a report from the latest 1.11.2 dev version -- stained glass appeared to work correctly in my test, although maybe non-vanilla items still have issues.

@Kobata Just tried 1.62-dev-80 and autofill isn't working when placing any vanilla blocks.
However, if I drop the items the autofill still works.

I tested placing stained glass, so it should work that way. Are you sure you're using the main hand -- offhand is still ignored as much as possible except where it directly interferes.