NGUI doesn't work correctly from asset bundles. It never had, and I'm surprised you didn't run into such issues before. I'm guessing its related to a global list of draw calls. I plan on changing it back to where each panel owning their own draw calls in the near future, so it should address this issue as well.
However as I said... asset bundles + NGUI is not a good combination.
Super weird as this only happens lately when building the bundles using an open scene that has ngui in it, not actually testing in editor or on device. Ive been using nGUI in assetbundles for a few months in a production game without any actual issues.
I think it might be something else causing the issue, possibly unity related, but was hoping to track this one down in the meantime. I get some weird "Fatal Error! CheckDisalowAllocation. Allocating memory when it is not allowed to allocate memory." error at random if I open up a scene with ngui, make some changes like rename some text in a label, and when i go to load another scene after saving the current scene it crashes with that error.
EDIT: Oh btw not really looking for an answer if there is none or normal use for unity will cause this issue now. I havent tried wiping out my local cache of the project and rebuilding or even trying on another machine or with any of the 4.3 builds on unity yet =)