Regarding boot09.itm (and other platform variants) when the equipping effect was added the # of equipping effects was increased, however the ability effect index was not updated. NI & DLTCEP do not report errors regarding this at least not in anyway that I can find.
You can read more about the discovery and what I used to track down this particular file here
This block in the aurora tp2 needs to be adjusted
from this
into something more like this (needs tested & could be 'cleaned up' to fit existing code writing style