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From your PM to me, you say nothing changed. So the only thing to do next is see what is different between good and bad. Take your good state, single sweep and leave in hold, save the state as a .csa file; if you see the problem again, hold the sweep, save the state as a .csa file. Post the two files and we can see why they are different.
You say everything is fine after preset, but then you don't say how it becomes bad. does it drift (you PM said no drift was seen); does it just jump, does someone set a magnitude offset? How does it go from good to bad, suddenly and unexpectedy while no one is watching? Usually, something must be done to trigger a state change. Maybe the step attenuator is getting flogged by accident without you knowing it? Is it a 5 dB step attenuator you have in that box? It would be an odd hardware problem, never heard of it before, but there's always a first time.
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