I am using Repetier-Host version 2.3.2 on Windows 11 Pro. I use Slic3r 1.2.9. with the "individual objects" option enabled, and it has always worked for me.
However, there is a new feature that moves the models when slicing. If I enable the "Try to preserve model positions" option to keep them from moving, it disables the "individual objects" option, causing everything to be printed on the same layer simultaneously.