Thanks for your feedback. Clippings should be able to save the order of the clippings when arranging them in the Clippings Manager tree list using drag 'n drop. Which version of Clippings are you using, and on which version of Firefox or Thunderbird? Are you trying to reorder the clippings at the top-level, or within a subfolder? Are the affected clippings inside the "Synced Clippings" folder?
As for the problem about the window getting smaller and smaller, are you referring to Clippings Manager? Which OS are you using (Windows, macOS, etc.)? I would like to investigate this further.