Hmm.. I don't know what the image order was previously and I don't know what it is now (alphabetical, date order, random) so it's hard for me to know what might be happening.
I'm a little unclear as to all the steps you've taken to get your new images into your existing gallery.
Is there any chance you could list everything you did in order so that I can better understand the situation?
e.g.
(1) Re-uploaded 'large' images to an already imported gallery's source folder.
(2) Re-imported gallery to obtain a new imported gallery (with new images).
(3) Copied all image size files from the new imported gallery to the original imported gallery's 'images' directory.
(4) Deleted the new imported gallery (which was only created to generate new images in all sizes) via Showkase's interface (on the 'Pages' tab).
I'm not sure if this is exactly what you've done.
If it is, then I can't explain why the image order would have changed. The gallery's XML file which holds all the image data (including image order) would not have been modified.
With regard to image titles and captions, you could maybe embed them within your images as IPTC metadata so that the titles and captions are part of the images themselves and they travel with the images. Wherever the images go, their titles and captions go, too. Showkase can extract IPTC metadata (a limited subset but enough for titles and captions) for use as titles and captions. You can instruct Showkase to extract the IPTC title and/or IPTC description for all images at once.
Please see 'Editing Individual Captions' in the Pages section of the Showkase User Guide for details on how to extract the image's IPTC title and description.
There are some special codes that can be entered into titles, captions and descriptions:
{iptctitle} causes Showkase to look for embedded iptc metadata in the image and insert the contents of the title field if present.
{iptcdescription} is translated into the iptc description field if present.
If entering IPTC data via Adobe Photoshop, {iptctitle} corresponds to the IPTC 'Document Title' field and {iptcdescription} corresponds to the IPTC 'Description' field. I expect these labels will be the same for Lightroom (but I'm not 100% sure).