I made a set and then got a new item and went into the set to change out the head piece for the new item. It seems to save but when I use the set it puts the head piece on for 1 second and then switches back to the old headpiece.
edit
ok I found a setting called enable auto queues which is on by default and turning that off fixed it. I have no idea what autoqueues are.

Autoqueues are a feature that can be enabled/disabled with alt clicking on slots (sse here https://www.curseforge.com/wow/addons/itemrack).
Just disable it again.