Alright, so I figured it out... For whatever reason Blizzard put multiple files in the FriendsFrame folder for the files in question, the afore mentioned IgnoreFrame-BotLeft.blp/IgnoreFrame-BotRight.blp which evidentally don't do anything and then UI-IgnoreFrame-BotLeft.blp/UI-IgnoreFrame-BotRight.blp. The later pair are what actually gets used by the game.
Was driving me crazy... maybe this will save someone else the headache of trying to figure it out.
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