related to flats - question regarding CR2 debayering and histogram

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shoot a flat (iso800, 1/32s, modified 50d against a lightbox)

1) set DSLR_RAW to raw bayer RGB image. using BatchFormatConversion, convert CR2 to fits, then use BatchDebayer to debayer the raw fits file using bilinear interpolation. all white balance checkboxes off.
2) set DSLR_RAW for bilinear interpolation, all white balance check boxes off.

in both cases, black point compensation off (check box checked)

when the debayered #1 is loaded and compared against #2, the histograms are completely different. the histogram of #2 is very strong, with the blue peak at 26%, green peak at 32% and red peak at 68%. the histogram of #1 has the blue peak at 5%, red peak at 7% and green peak at 8%.

is this expected behavior? or is my flat overexposed and somehow confusing BatchDebayer?

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i did some more experimentation with this. with respect to dcraw debayering, the relative channel ordering in the histogram depends on whether or not you tick "no black point compensation". this makes sense, i guess.

however, i still don't understand why the histogram looks so different between the script-debayered version and the DCRAW-debayered version. in fact, at least when calibrating a CR2, the histograms of a debayered light subexposure with and without black point compensation are the same.

i was trying to run the SkyLimitedExposure script on a calibrated CR2, but the script comes up with 0-e for the background flux in the calibrated fits file. the script comes up with something reasonable if i load the raw CR2 with DCRAW and use bilinear debayering, but the result probably is not accurate because the CR2 is not calibrated.

i'd suspect my calibration masters were screwed up except that i see the same 'low signal' behavior simply by converting formats as described in the previous post.

have any other DSLR users seen the same behavior?