Ok, I found the problem.
Reordering the issues within a title "modifies" each issue, and the modification was triggering Comicster to re-download that issue's thumbnail image. So reordering the issues was effectively taking as long as regenerating thumbnails for the entire title would have.
I'm publishing a new version which temporarily turns off thumbnail generation while issues are being reordered. This is the first version I've tried publishing from Windows 7, so fingers crossed!