Like David, I'm far from an expert, but would like to assist if possible. Could you post a raw Ha sub, and maybe the stacked Ha? What gear (scope, filter wheel, coma corrector/flattener/reducer, camtrain dew heaters, etc) are you using, including brand? Also, what were the conditions (temp, dew, etc) like when you were shooting?
I've had my 1600mm-Pro for only about 13 months now, and have made a lot of mistakes with it. And, I've only been imaging for a little over 2 years. So, I'm not an expert by any means, but I have produced subs similar to your OIII subs in that short time.
Possibly your OIII filter had some dew on that quadrant. I've had a few occasions when a particular filter, always the one that is in the light path in the camtrain when cooling down the chip or one directly adjacent to that filter, get dewed up. Those times, by moving to a different filter, especially one on the opposite side of the FW, I've sidestepped the problem till the problematic filter dried off. I think I've read several places here on CN that under damp, cold conditions, cooling down the chip too quickly can cause the optical element that is nearest to the camera during the cooling (typically the filter that's inline) to fog over (dew up). I think that this is a result of the heating of the front glass on the camera. I've rearranged the filters in my FW such that I have an L-Ha-R-OIII-G-SII-B arrangement, so that if I have to switch filters due to dewing, I can usually continue shooting as before (NB or LRGB). More importantly, I do my cooling in stages, usually 5 degrees at a time, till the cam chip reaches the desired temp. This staged cooling is also something I've picked up here on CN. Since I started cooling in stages, I have not had a single instance of a filter fogging over.
I would definitely do as David suggests, and check the filter seatings in the FW as a first step.
While this is most likely unrelated to your posted issue, it appears to me that you need a better coma corrector, or need to adjust the spacing between the corrector and the camera chip, though this probably has nothing to do with your problem. Also, since different filters (say Ha and OIII) typically seem to have different vignetting and other issues when used under otherwise identical conditions, whatever issue is causing the OIII subs to come out this way might not show up in the Ha subs as noticeably or at all, but still be present.
Hopefully this helped. If not, there are folks here on CN WAY more versed and experienced in AP, and folks WAY more knowledgeable in the 1600, than I. Such as Jon Rista. I hope some of them come to your rescue, and correct/teach me as well.