Cura Multi-Color Printing Preparation Failure

[Alex-Samra 0]

I am trying to merge two parts in Cura to print in two colors on my Ultimaker S5. I have followed all of Ultimaker's recommended steps seen here, preparing the files in CAD to align on the same coordinate frame and making sure to select this coordinate frame in the options tab on the file export window. First, when I exported in STL, I had parts that were centered on the build plate but dropped down, and merging them resulted in a random alignment with the logo text sticking out of the middle of the cylinder. When I tried 3mf and other file types, the origin reads correctly and places both files in the correct place spatially, but when I merge them it puts a massive gap between them and tilts them to the side for some reason. I have had several coworkers try this export and merging process with different design softwares and filetypes and origin setups, and we all have the exact same issues in Cura no matter what, so it seems to be a Cura-related bug. This is an important capability for my job shop so we need to get this figured out quickly.