A couple of days ago I upgraded from the March version of NGUI and suddenly my buttons stopped working during screen fade in/out events.
After a lot of investigation this seems to be a problem that's resulting from Unity providing invalid responses to touch/input events. While I can't find the precise cause of NGUI getting bogus input states, I was able to work around the issue by identifying my input objects within the NGUI code and forcibly setting the click-state to true when one is encountered. Yeah, I had to hack the NGUI code to deal with this.
Basically I've added a check to NGUI that says "if a collsion object has a specified prefix then ALWAYS treat it as being a valid collision (button press)". Doing this has eliminated the non-responsive button issue, but only works because I went to the effort of insuring all my button GameObjects had "bt" prepended to their names.
So, likely a Unity issue, but certainly one that everyone should be aware of.
Nick