Bug 1100 has documented this issue rather extensively. The summary is that BBCooker.collect_files() reads the file globs in the order they are listed in bblayers.conf, but does not attempt to generate the files and appends lists with layer priority in mind. The expectation is that a bbappend from a layer of priority 6 would override any setting it had in common with a bbappend from a layer of priority 5 or lower.
Patch send to ml: https://lists.yoctoproject.org/pipermail/poky/2011-May/006520.html
Patch has now been merged: http://git.yoctoproject.org/cgit/cgit.cgi/poky/commit/?id=58bdecbc43390796e7050ad9e0033176716ec423