When I guide, I watch the graph and it is as you described. it will go from close to zero to over 1 sometimes 2 pixels. But I would expect this with the seeing I have here in Queanbeyan. Also imaging at .6 arc seconds per pixel every fluctuation in the atmosphere looks huge.
I haven't done any imaging in the past two months because I have been away.
The last image I did was a twenty minute guided exposure, and I remember watching the graph and it was fluctuating all over the place. The end result was quite acceptable.
What do your final images look like? are the stars eggy?
One thing, when you are capturing your PE data does the guide star stay well centred or does it drift away?
Also as Marcus has said the longer the better, I use at least 20min worth of data for PEC.
Cheers
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