i need to go read itelescope's descriptions, but i think what's going on here is this: i21 has a rotator. there is a meridian flip involved here (i assume that's what the W and E means in the light filenames) - since the orientation of the DSO is the same between the E and W-named images, the rotator turned 180 degrees after the meridian flip.
that's fine, but it means you need 2 sets of flats; one for the E side and one for the W side, since the camera orientation changes when the rotator rotates. all the flats provided in the dropbox are for the E side; the W side is missing. calibrating the W lights with the E flat is probably making them look absolutely awful given how crazy those flats are.
also it looks like one of the lights is misnamed - E-180-009 looks like it should have been named W-180-009. also if the "180" is supposed to represent the rotator position angle, then something went wrong in the file naming at iTelescope because half of the images should have PA = 0.
anyway, i assume that's the source of your troubles. i guess for now you can just calibrate and stack the E images.
rob