The Essentia terminal view is overlayed by NEI and therefore disturbing to use. I tended to disable NEI while using it but I guess its also worth a bug report.

Related Settings: 1680*1050, GUI size: auto.

Essentia terminal view is: http://i.imgur.com/1vPWOJx.png

Regular AE² crafting terminal view for reference: http://i.imgur.com/Vg1se4v.png

As a sidenote, the arcane crafting terminal does not have this issue as well.

Honestly don't know how to go about fixing this one. Would need to look into NEI's API and see if there is a way to let it know when my GUI is taking up the screenspace.

Was doing a lot of funky math in that GUI class for no reason. The issue ended up being that the GUI wasn't centered vertically.