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Hi Graham,
To get rid of any green hues in ST, lauch the Color module and set 'Cap Green' to 'Yellow' or 'To Brown'.
Not sure if you have taken this into account, but do keep in mind that even though your frames are all the same duration, the actual light gathered per filter can vary substantially. Therefore you should find out the right ratio to multiply your exposure times by for your particular filter set and CCD sensitivity for the different wavelengths.
If you don't know the right ratios, you could find out by calibrating against a known object (for example a G2V star).
Cheers,
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