When you come back to your home server from battlegrounds, much of the UI gets reset -- that's probably when that window is being unloaded.
I notice it in Fetish because the stat bar always pops up and my chat channels always end up in my main chat tab. It's really annoying how it reloads it, and I've /bug'd it a few times in the hope that they can find a better way of transitioning between the servers without forcing the UI to reload that way each time.
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