Hi Mark.
I had another look at just the red, green and blue singles, the pixel count, pixel size (binned) and sensor format is consistent with an Atik 314L (6.45um x6.45um 1391x1039) however loading the three frames into PI's subframe selector and looking at the image statistics it appears that the filter wheel did not move between the various filters, the statistics for the three frames are almost identical.
The FITS headers for the three subs states that they were indeed taken with red, green and blue filters selected but the statistics for the frames, and particularly with that target, shows (I think) that the filter wheel did not physically move between filter changes.
I do not know APT but possibly something was not correct in the equipment setup, or there is a problem with the filter wheel itself.
Verify that the filter wheel is working correctly and that APT is moving the correct filters into position when requested.
The only other way you could end up with almost identical red, green and blue integrated frames is if the individual frames in each integration were mixed up and you had some red frames mixed up with blue etc when you integrated the individual colour stacks of subs.
Try taking a single uncalibrated raw sub of each colour, star align and then colour combine. The resulting image will be noisy and weak but strong colour should be present. If colour is present then go back and look at the individual subs used in the integration stacks to make sure they are not muddled.
HTH
William.