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Sometimes, the channels plotted and the window titles/legends get mixed up, so while I think I'm looking at one signal, it is in fact a different one (e.g. plot legend might say C1:LSC-CARM_B_IN1 is being plotted whereas the signal is actually C1:LSC-DARM_B_IN1). Often, the signal characteristics are different enough that one can clearly identify that there is a problem, but sometimes, several painful hours can be lost before realizing that this is happening.

I've personally only observed this when starting up from a yaml file, I'll make a note if I ever happen to see it when launching with the channel list as the command line argument. I haven't seen any clues as to what could be the underlying cause, will update if I do.