Walt,
Try Helicon Focus on the same stack. CombineZM has trouble handling stacks that have detail at the same place in multiple depth planes, at least using its Do Stack macro. That's because Do Stack tries to fit a single-valued depth surface to all the places where it finds detail. That's not a very good model for many transparent subjects, and the way it typically fails is by producing kind of "swirly" artifacts like I think I see here. Helicon Focus uses a completely different model apparently involving local weighting based on sharpness, with no depth surface at all as far as I can tell. (HF's model has its drawbacks too, but swirly artifacts are not among them.)
Those color fringes are interesting. They look like some kind of CA, but I don't think they're classic LCA (lateral chromatic aberration; also called CDM, chromatic difference of magnification) because the fringes are present even at image center. How do these things behave as you go in and out of focus?
One last question/comment/suggestion is about your focus step size. What's the NA on that objective, and did you really need to stack so finely?
(Hhmm, that's 2 questions. Oh well.) The reason I ask is that
http://www.microscopyu.com/articles/for ... depth.html doesn't get down to 1 micron DOF until 40X NA 0.65, and I think they're spec'ing it for finer resolution than we'll see here in the forum. I have vague recollections that stacking too finely may cause problems at high mag, though I never studied it enough to really understand why, when, or even if, in general. Anyway, if it does appear to be oversampled (too finely spaced), then you might try processing a shorter stack using just say every other frame.
--Rik
I download CombineZM yesterday and gave it a try (numerous times), since it was free and I had nothing to loose, I did not like the results either. So I ditched it. Maybe I will try it again later, I dunno. 
