I cann't reproduce this here. Take a closer look at what you are seeing. You are not seeing a random FX window - it's just some other window that was already open.
If it is confusing, you should check in
Options > Prefs. > Plugins "allow only one FX chain window open at a time"
If docking FX, this really is the only option that makes sense.
Floating FX windows ignore this when clicked on from the MCP - so checking this dosen't mean you'll never be able to have 2 plugins open a at the same time - just never 2 docked chains.
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