When assigning a Job Code, the file jumps to the bottom when some columns are used to sort with

The images are ordered by date, unless there is a problem detected in the scanning, in which case it is then organized by status, with errors at the top, followed by warnings. The only exception is if the user clicks on a header as the scanning occurs to sort it themselves.

You need to use a different theme if you want vertical lines, or alternating horizontal colored lines. This is not something controlled by Rapid Photo Downloader.

Hmm, on attached picture you can see index of card just after inserting and scanning, no clicks were made, only scrolled. I tried it several times, with different card from different cameras - it looks like order is random. No errors displayed.
May here is the key: if I click on JC or File type column (when no JC given and all images are JPG), images are resorted with random (?) order. The fact that they are resorted without criteria is a bug itself.
Please, reopen this bug, may be someone else will confirm it and give some details.

About theme - do you mean Ubuntu appearance theme? In my current theme alternating horizontal colored lines are used (at least Nautilus and file dialogs has colored rows and columns).

More testing:
- mounting card
- run RPD (upward arrow appears on status column)
- assigning JC -> images get resorted (each time you assign JC), last tagged images get to the end of list, no matter which letter JC begins with

Rapid Photo Downloader uses the theme default for any coloring of columns or rows. Please contact the author of your theme if you have any questions about that.

When assigned a Job Code in the main window (using the drop down combo box), the selected files jump to the bottom when the status, type or Device columns is active as the default sort order, i.e. where there are duplicate values in the column being sorted with.