Troy,
When you've got your camera hooked up to the telescope, does it still work in Av mode? Because, you can't really dial in an aperture value... or, can you?
If it works for you, there's no reason for you to switch to manual.
Geoff, doesn't matter if the image isn't uniformly grey. When you flat divide, the software takes care of all of that for you (greyscale division). I've used flats which have had a slight red and blue cast to them before. No problem, as I don't convert them to CFA in IRIS -- just divide by the raw... RAW.
Hope this helps.
Regards,
Humayun