With respect to the observation that "exposure change resulting from changes in light levels as the sun hides behind a cloud", I also find this occasionally.
For context: I shoot D300 RAW, convert RAW to 16 bit .tiff in ACR (Photoshop Extended CS4), and pull the .tiff into PTGUI. All processing is done on an oldish MacBook Pro. My overlaps are usually 25% or more, can go as high as 50% under operator error.
Here's what I do to "correct" exposure differences when they propagate through the PTGUI blender and compromise the resulting panorama:
1. Review image in PTGUI Panorama Editor in the "Preview without Blending". This makes the tonal variations between overlapping images visible, especially when they're large.
2. Working one source image at a time, identify images that exhibit large tonal shifts. Keep the project open in PTGUI, and stand by for some PTGUI magic: delete the offending .tiff, pull the source RAW into ACR, and adjust exposure up or down as appropriate (this is a guessing game), and create a fresh .tiff directly from ACR to replace the one you just deleted. Hurry back to PTGUI, and you will see PTGUI refresh the panorama when the new .tiff is available (magic!!!). Repeat as needed.
I delete offending .tiff files because ACR will use a different name for the new .tiff if the old one is still around. My ACR does not overwrite the pre-existing .tiff. If you prefer to keep the offending .tiff, you have two options: a) move it out of the current directory, or b) go to the "Source Files" tab in PTGUI and replace the old .tiff with the new one.
You guys probably know a thousand variations on this theme, hope you find this useful.
Joost, does this PTGUI magic also work under Windows?
Regards