Every time I mount up on a mount in skyriding mode, the usual action bar appears as expected but the abilities keep rearranging themselves. Bronze Timelock especially just keeps moving itself to the third slot no matter where I put it, and mixing the rest of the abilities up in the process. Changing characters, dismounting and remounting and simply logging out and back in seems to cause it. I don’t use any addons for action bars, so I’m not sure what’s causing it.
Bump. Been happening since I got Lightning rush.
I am having the same issue. I am constantly having to setup my Skyriding Action Bar back to the way I want it, and then it changes again within a few hours. It seems to ALWAYS want to add Bronze Timelock back into my bar.
Similarly to the OP, I seem to notice it when logging out and logging back in.
Bump. Same issue here, though it seems random character to character. Bronze Timelock to the third spot as others. I don’t use it and put Skyward Ascent there. Pain in the tuckus!
Ok, I took the Bronze Timelock off the bar and logged out disabled all addons and came back and it there it was again in some random spot on the skyriding bar. So it’s not and addon doing that. So put it in some random spot on my bars but off the sky riding bar and it stopped moving and doesn’t reappear on the skyriding bar to mix everything up and cause chaos. 
Does work if you put it on a hidden/disabled bar as well. It should be noted that I have an addon that disables auto add spells, and that did not stop this from happening.