Ahh, I think I see what's going on here. It seems like it sees that there is already a user defined coordinate system at that exact position and orientation and doesn't create a new UCS, but instead references the existing UCS. The net effect is that both features in the timeline are for the same UCS entity. You can edit the first feature and the UCS will change, but if you do Modify -> Compute All it will update to the second feature in the timeline.
If you create two UCSs at different positions all is well, but if you edit one and change it to the same position and orientation as another UCS it will irreversibly be combined into one UCS. It seems like if you have anything referencing either UCS it will not combine them, which is good.
I'd still say it's a bug, but not that big of a deal.