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Hi Ben,

A few ideas for testing:

1) if you quantify the average intensity of a few objects in the affected zone versus outside, do you get roughly the same values? If not, I wonder if Michael is correct about a streak of oil somewhere. Depending on the Zeiss microscope stand, there could be oil on the sideport prism (do you see an artifact by eye, for instance?) or it could be on the protective glass over the filter turret, if this is an old AxioVert 200M (which means oil got under the lens). 
2) Is the affected zone the same proportion of the image when you use a different objective? Or does this zone change size, or disappear completely?
3) Try turning off interpolation on the screen (in ZEN black, it’s under the image), slow the scan speed way down (not to the limit - might introduce other issues) and decrease the number number of scanned pixels (256x256 perhaps). As you watch each pixel get scanned, do you notice anything funny happening in the Y-axis? Maybe your galvo is not stuck but slowly sagging and then jumping back up to position in that region of the scan. My best guess is this might mimic a lensing effect, which your images look like in some ways: the objects look a little like a speed bump from top to bottom. (Lensing might also come from a streak of oil, too.) Try a second scan also at slow speed but with many pixels - any improvement? 
4. Rotate/unscrew your current objective a quarter turn. Refocus, and rescan. Is the issue occurring in the same orientation? 
5. Introduce some line skipping. Does the affected region stay the same proportion of the image field, or does it, too, get wider? 

Let us know!