After rebuilding my gallery, I have just unzipped them to over write the new versions, and bingo the sort order is restored.
Good thinking! That'll work.
As a matter of interest, your multi-tread explanation does seem to fit. I couldn't replicate the problem on shared hosting today...
Yes, this theory does seem to make sense.
I have no doubt messing about with the showkase directories and content is generally a very bad idea and is frowned upon...
Not frowned upon... just not officially supported.
Having said that, if you really want a button to regenerate only images and don't want to create one yourself (I don't know how many source files would be involved) or wait to see if the developers introduce one, then you could maybe re-purpose the existing 'Rebuild' button to process only images by commenting out the lines of code which deal with regenerating the accompanying text files.
A couple of caveats:
(1) You'd no longer be able to use the 'Rebuild' button for its original purpose/full functionality.
(2) It would work only if no images are added to or removed from the gallery and if all filenames remain exactly the same. (I know you are aware of this. It's worth mentioning again, though, just in case anyone else is reading this.)
With this in mind, if you want to try it out, open your site's admin/commands/advanced.php file in a plain text editor and comment out (or remove) lines 77 to 86 (inclusive) and also lines 88 and 89. You can comment out lines of PHP code by adding // at the beginning, as follows:
// $page->gallery->saveGallery();
// Board::addMessage('Gallery xml file rebuilt');
// $pageSet->setPagesDataImageCount(
// $pageIndex,
// $page->getImageCount()
// );
// $pageSet->savePagesData();
// $pageSet->setPagesPref('publishing', 'unpublished');
// $pageSet->savePagesPrefs();
// Board::addMessage('Page data cache updated');// $page->savePageHtml($pageSet, new Nav($pageFactory, $pageSet), new GalleryIndex($pageSet), new Smarty());
// Board::addMessage('Page html rebuilt');Just re-upload the file after editing it (to its original location, overwriting the existing file). You might like to make a backup of the original file first (although you could always just extract the stock version of the file from the Showkase zip file if you need it).
This is untested and, being a source code modification, as far as I can take this in my capacity as official support.
I hope it points you in the right direction, though.