Matthew is not alone with this particular complaint. I make large panoramas to print, and banding in the sky is the bane of my existence. Most of my panoramas are cylindrical projections composed of two horizontal rows, each comprising 20 to 45 frames. The vast majority of problems I encounter is sky banding in the top row. I spend many hours (understated, if not accurate) micro-adjusting the exposure and color balance of the RAW images in an attempt to eliminate the banding. I use Bridge to dump the .CR2 files into the Photoshop Camera RAW Viewer. I watch the histogram as I move between frames--in particular, the blue line on the right side of the histogram. Large jumps in the histograms' blue lines invariably indicate the positions of the beginning or end of severe banding. Where the sky changes from light to dark, or vice versa, I strive for a smooth, even transition in the histograms. A small (or sometimes, not so small) adjustment to a frame's exposure can reduce the size of the blue line jump and improve the final sky rendering (small changes to the temperature are a secondary option), without adversely affecting PTGui's ability to blend the image successfully. This can be a painful, time consuming process, as I then convert the RAWs to .TIFs, rerender the panorama, and search for more unacceptable spots. Please understand, I undertake this effort only when necessary. My first rendering of a panorama is made from a set of .TIFs whose RAW frames have had minimal but usual and reasonable adjustments made to them.
Some things that may help, when help is needed: reducing contrast within the camera itself, if available (contrast can be increased in the final image, after blending occurs); choosing a less saturated Camera Profile during RAW processing (Camera Neutral will usually produce less banding in the final image than Camera Landscape, and saturation can be increased in the final image, after blending occurs); avoiding the addition of too much Dehaze Filter (sometimes, some is desirable, but it can exacerbate banding; unfortunately, Adobe imposes size restrictions on the availability of the Dehaze Filter, and it may not be available to use on the final image); ignoring the Vignetting correction in Camera Raw and instead eliminating obvious dark corners with the Spot Removal Brush; masking the sky with the Adjustment Brush and then selectively changing the exposure of only the sky (to reduce large blue line jumps in the histograms of adjoining frames). I would also suggest scrubbing the rendered output at print size. The transition from light to dark will often be more gradual, and therefore more acceptable to the eye, than that viewed at thumbnail or fit to screen size.
The idea of uneven shutter motion had not occurred to me. I normally photograph at f/11 and somewhere between 1/320 and 1/800 of a second. I will slow it down and see what happens.
I have noticed that the shape of the layer masking in the final output of PTGui often employs straight vertical lines with doglegs (zigzags) at the top and bottom. I wonder whether a "drunken jigsaw puzzle" edge, more like the one used by Photoshop's Photomerge, might not be a serious improvement worth requesting. Photomerge seems to color-blend the edges, where pronounced banding occurs, more gracefully than does PTGui. Photomerge, however, has its own unique set of problems that makes PTGui my goto software.
Serious panoramography is neither for the faint-hearted nor for those in a hurry.
Best Regards
Rob