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Hi Graeme
If your tracking and guiding are good, I would go for a longer exposure, mine was a total of 50 minutes, 5 x 600 secs @ ISO 800. That blue smudge has all the hallmarks of an internal refection so it is interesting that it corresponds to another mark. I make a habit of using a blower to remove any residual dust from things prior to taking any shots, may be a worthwhile step to take.
As far as flats are concerned, it dosn't make any difference when they are taken so long as the telescope and camera are in the same orientation, the shots are so short it makes no difference that I can see.
I don't know if you do it or not but, all my shots are RAWs, Lights, Darks, Flats and Bias, I then use ImagesPlus to combine them in the Automatic Proccessing routine, I don't convert to Greyscale.
Cheers
JohnG
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