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Only problem is that when I have NEI Syncronized Auto on, it sometimes does not react to the searching at all, sometimes it takes very long time... What does this depend on?
It's just client load. Many loaded chunks slow down NEI, and the AE interfacing with it was slow to begin with. NEI is low in the priorities, so it's gonna become slow if anything else is happening.
For me, it only seems to be taking that long if I have filtered NEI subsets (with the button at the top of the screen). When that is cleared (I think double left-click clears it), searching is fast.
you can right click (or was it shift right click?) the mod name (or sub menu) from the mod selection screen that will filter out all of the items in there
you can save these selections by right clicking the top button