I've just discovered an interesting issue and curious to know if this is something happening locally on my machine or others have also encountered the same problem. The issue is when I lock a properly weight-painted layer, any adjustment made to the next joint's weights manages to slip additional influences back into the locked layer. This seems to be happening when most of the other layers are locked.
The last time I ran into something a bit similar, influences that were removed or scaled down would get moved to the unlocked layers. But now, it looks like locking isn't doing anything. I've restarted Maya but the problem still exists. I was wondering if there is a way around this? Any tips/tricks anyone can share is greatly appreciated.
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http://www.ngskintools.com/
edit: I noticed you mentioned layers yourself. We're still using maya 2012 so autodesk may have added something similar. However, the plugin I listed is excellent, and has a bunch of other great features as well.