Chase,
As long as the filters are being centered by your filter wheel, the kind of edge vignetting that you are seeing has nothing to do with the filter itself--or the exposure time. The effects may manifest slightly differently with respect to glancing stray light at different wavelengths but that's a red herring. What you are seeing is due solely to the
geometry of the apertures in the optical system, which determines how much light makes it from the entrance pupil onto the sensor. In your case, the size of the apertures or the component spacing is simply blocking too much light in the corners of the sensor. Flat calibration removes a lot of this stuff but it can only handle so much vignetting before noise issues and small errors in the calibration data start to cause problems. My own rule of thumb is to try to keep the amount of vignetting in the extreme corners below about 30%. With values over 50%, there is almost always going to be trouble. You can measure the amount of vignetting that you have simply by measuring the ratio of the signal in the corners of your master flat to the signal in the middle--obviously using linear data.
General rules of thumb to avoid this problem are to use the largest possible diameter for adapters, adhere to the correct back working distances for each component, and make the spacing between components as tight as possible. For example, the spacing between your FW and sensor should be as small as you can possibly make it--and you should double check with a drawing (or a calculation) that the marginal rays at the edge of the field (called y + y_bar) are not being blocked by the filter.
I also want to mention that the other thing can will screw up image calibration is stray light. Remember that flat calibration only corrects for multiplicative effects, which are: Vignetting, cosine to the fourth radiometric fall off, and PRNU. Stray light is not multiplicative. It is additive. Therefore if you have small strays that are generated from glancing reflections from inner surfaces of your adapters, they will not be removed. In general, image calibration tends to make stray light look even worse. So, it is extremely important to make sure that the interior surfaces of your adapters have glare-stops along with highly efficient anti-reflection paint. For most amateur gear, glare stops often consist of threaded surfaces (which are quite effective) but many use standard hardware store level flat black paint that isn't very good.
Finally, you can assess the level of vignetting in your system by pointing the telescope at the sky during the daytime. Remove the camera and put your eye roughly where the sensor sits and look backwards through the telescope. If you move your eye to the edge of field, you can often see exactly what is blocking the light. You can see what that looks like when I did the same thing with my 20":
https://www.astrobin.com/xfedon/I/. In fact, that might be a good read to better understand this issue and how I solved it when I ran into the same problem you are having.
John
