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I think I've fixed my flats issues. Just had a play around with the filter masks first and that seemed to have changed a few things.
Also changed the exposures for two of my filters (SII and OIII) and I'm getting much nicer flats now. I had to bump them to 11 and 6 seconds respectively.
I only have one issue left and that's an issue on my OIII where one corner is very bright. I think it's the edge blackening of the filter that has rubbed off and light is leaking in, d'oh. Need to do more tests.
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