Hi, I recently tried to install NotEnoughItems and In-Game NBTedit. However, I was running into an issue where FML and CodeChickenCore worked fine, but NEI was completely ignored like it wasn't there. (I didn't install NBTedit yet.) I'm using the recommended universal FML build and everything involved is at 1.5.1. I found a few relevant lines in the log, especially line 85:
Line 58: 2013-04-10 17:25:05 [FINE] [ForgeModLoader] Found a candidate zip or jar file NotEnoughItems 1.5.2.9.jar
Line 63: 2013-04-10 17:25:05 [FINE] [ForgeModLoader] Examining file NotEnoughItems 1.5.2.9.jar for potential mods
Line 64: 2013-04-10 17:25:05 [FINER] [ForgeModLoader] Located mcmod.info file in file NotEnoughItems 1.5.2.9.jar
Line 85: 2013-04-10 17:25:05 [iNFO] [ForgeModLoader] FML has found a non-mod file NotEnoughItems 1.5.2.9.jar in your mods directory. It will now be injected into your classpath.
This could severe stability issues, it should be removed if possible.
Full log: http://pastebin.com/erLKFM3M
EDIT: Turns out that this only happens to NEI, and not NBTedit. However, this same issue happened to me before while making a modpack and it ignored ALL mods. Unfortunately, the log for it is long gone.