I tested issue #3069 with version 1.7.10-8.1.8.261 and in this version Shift+Click on item not working.
When I click on the item (e.g. Iron ingot), nothing happens.

Edit: I tested it again and I found out this:
Items for Infusing (coal, redstone,..., compressed items) is still going to wrong slot (for input items) and infusing items (iron, alloys,...) absolutely not working.

I have the same issue expect iron ingots go to the output slot and then get pulled back into my system

If you have this problem, imho you have older version. This problem I had in version 1.7.10-8.1.8.258, but in 1.7.10-8.1.8.261 I only have this problem with items for Infusing (coal, redstone, etc.).

Fixed in dev