Pattern Encoder 'Encode' button is at the same place on screen as NEI '?' button, which sometimes results in unwanted encoding when a player presses Shift+'?'.

It might be mouse tweaks. I tried with Inventory Tweaks and don't see that behavior - the pattern is taken out on mouse down normally, not up.

I'll play with how the gui is layed out when i have the time, but you should report it to Mouse Tweaks author.

Thank you. I just wrote to the author of Mouse Tweaks, hope he responses aswell.

Don't press the button twice? :P

I don't see any better way to arrange that UI, moving them to the left looks weird.

It's not pressing button twice. If your mouse button isn't released when the Encoder screen pops up, you instantly pick up a pattern. It only happens with shift-click though, like you are able to move items between inventory and chest - just hold the 'Shift' and mouse buttons then simply move your cursor above items. Yet it is annoying you need to watch where you are clicking (down half of '?' button). Maybe move it up just slightly, decreasing that arrow size?

Edit: I have Inventory Tweaks an Mouse Tweaks mods. That maybe the reason you cant replicate this problem?

I've tried and can't find a setup that i'd like where that slot will not intersect the ? button in NEI.

Hopefully Mouse Tweaks dev(s) will be able to fix this on their sides.