I'm running an FTB client on a secondary monitor, and when opening the NEI interface, I am unable to use the sides or top of the screen (items at the edge of my screen can't be moused over or interacted with), though the mouse pointer is still capable of entering that portion of the screen. NEI works fine on my primary monitor, and I can use buttons related to other mods in that section of the screen.
Does anybody know of a way to fix this?
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I would suggest trying out TMI, just as a test, see if it works normally on the secondary monitor, or really any other mod that has portions of it's GUI in those areas.
If the problem is limited to NEI, I would bring it up in ChickenBones' thread and hope he sees it and can find a fix.
If the problem happens with all mods that have extended GUI's, you should try adjusting setting in your video control panel. What settings I can't say, gimmie a week or so and I'll have my secondary monitor and I can test it out, but for now I couldn't really say.