hi jerryyyyy
sometimes 2 passes of DBE are necessary. i'm not sure how much 'noise' enters the situation here - the backgrounds generated by DBE are synthetic 32-bit images. however as you get rid of gradients the amount of low SNR area you can expose gets better and so it may seem that noise is increasing.
are you taking flats? even if you have a focal reducer, flats are the right way to get rid of that vignetting. if you are trying to get rid of optical vignetting with DBE you'll never have as good a result as just using flats.
what is the origin of the images you have cropped? are you saying they were stacked in another program? or are you talking about cropping your subexposures? TIF vs. FITs should not matter for 16-bits, but if you are talking about integrated images it's probably better to save them in 32-bit floating point format. 16-bit images do not have enough dynamic range to capture all the tiny pixel values in an un-stretched, integrated image.
not sure about optimal sampling but the advice i've seen around here is to at least get the 4 corners of the frame if possible, and maybe the centers of the top, bottom, left and right edges.
rob