This is a weird one...it's popped up occasionally over the years, and it's hard to reproduce intentionally. Something similar was happening in my game for a while, and it just kind of went away.
You say it stops when you disable both plugins, does it stop if you disable just one?
Which class IDs does it happen with (and is it attached to the classes, not the actors? If you change the actor's starting class in the database, does it stop for them?)
Class ID's affected: 0001, 0002, 0003, 0004, 0005, 0007, 0008, 0009, 0011.
Actor ID's affected: 0001 "no initial equipment can be added." 0002 - 0004 " initial equipment can be added but (chest type) will always spawn as armor 0002.
Disabling the equip core or the item core separate from each other causes the issue to persist. Disabling both the equip core and item core resolves the issue. I've tried disabling all and turning them back on 1 by 1, and I have tried disabling requisite plugins to the pre-requisite plugins. Also vice versus.
Plugin Order: Community_Basic, MadeWithMV, Core engine, message core, x message eval text, key name entry, key number input, battle engine core, damage core, item core, item discard, item requirements, shopmenucore, more currencies, skillcore, limited skill uses, skillcostitems, equip core, equiprequirements, weapon animation, weapon unleash.
Following Yanfly's plugin order recommendations from
http://www.yanfly.moe/wiki/Category:Yanfly_Engine_Plugins .
I have made no changes to my plugin files except for YEP_WeaponAnimation which now calls /img/weapons in place of /img/system.
I have 3 <Not Independent Item>.