George,
Yep, these look like issues with the lens. At least with these subjects, it does seem that your lens is not working as well in this mode as mine does.
Any chance you can post out a full-size image and link to it? I'd like to see what the central portion looks like, and how fast it degrades away from center. The insect would be a lot better for this purpose than the screw thread, since I'm pretty sure it will have detail at a wide range of scale down to finer than any lens can resolve.
The markings on your objective mean that it's 10X with a Numerical Aperture of NA=0.25, designed for a tube length of 160mm and a cover glass thickness of 0.17mm. Tube length 160mm actually translates to 150mm from the shoulder of the mounting threads to where the image focuses -- the sensor plane in your case. There'll be some degradation from using the lens with no cover glass and with slightly wrong tube length, but I'm not sure how much of the problem is due to that and how much to something else. "Plan" indicates a flat-field correction, helpful for regular microscopy, but not necessarily an improvement when stacking because conceivably the flatter field comes at the cost of making other aberrations worse.
It might be informative to photograph some subject that has nice fine detail, and compare it to what you can see with direct view through the microscope. I'd recommend something like a moth wing -- fairly flat, good detail, not too shiny. If you can see much better directly through the scope, say with more detail and no color fringes over a wider field than the photo, that would suggest that the objective is designed to work with a highly compensating eyepiece and isn't going to work with direct projection onto the sensor. You could also do a check in reverse. Use your microscope eyepiece to look at an image formed by one of your enlarger lenses. If you see color fringes through the eyepiece that the sensor doesn't pick up, again that would suggest a significant eyepiece correction.
Just to check, do I have it right that these are with your Nikon D200, sensor size 23.6 x 15.8 mm?
--Rik
PS. (Edit) I reviewed some earlier postings at
http://www.photomacrography.net/forum/v ... .php?t=676. I see there that I suggested attacking the CA in your images with PTlens at Red-Cyan = -0.0040 and Blue-Yellow = +0.0060. I checked again with some images from my 10X objective, and the PTlens correction is only around Red-Cyan = -0.0018 and Blue-Yellow = +0.0019, less than half as much as for yours. Assuming those numbers are right, that could have a significant effect on delivered resolution. While PTlens or any similar post-processing can eliminate the obvious color fringing, it can
not eliminate the smearing within each R,G,B channel that is caused by chromatic aberration interacting with a broadband light source. That just turns into resolution loss. A compensating ocular fixes both problems at once.