With GT6, every time an inventory GUI (such as the player inventory or a chest) is opened, the item list is recomputed. This has a noticeable impact on performance. About 150 MB of garbage is allocated on the heap, and there is a ~10% increase in CPU usage on my machine (but at least it's on a separate thread).

With GT5u, the issue doesn't happen - the item list is only computed a single time.

Graphs

Code analysis

The issue happens because GT6 calls codechicken.nei.api.API#hideItem to hide items inside the getSubItems method of some of its items (PrefixItem and PrefixItemBlock). This causes the item list to get invalidated while it's in the process of being built, leaving it dirty forever. For example (printed by a debug print I added to the method):

markItemsDirty called. stack trace:
java.lang.Exception
	at codechicken.nei.LayoutManager.markItemsDirty(LayoutManager.java:581)
	at codechicken.nei.api.API.hideItem(API.java:134)
	at gregapi.util.ST.hide(ST.java:956)
	at gregapi.util.ST.hide(ST.java:946)
	at gregapi.util.ST.hide(ST.java:942)
	at gregapi.item.prefixitem.PrefixItem.func_150895_a(PrefixItem.java:128)
	at codechicken.nei.ItemList$1.execute(ItemList.java:205)
	at codechicken.nei.RestartableTask$1.run(RestartableTask.java:25)

Huh