In BambuStudio if you turn on “Flush into this object” (only configurable when prime tower is enabled), the slicer for some reason only generates with 1 color, usually the first color. Fix this by turning off “Flush into this object”, this option will be greyed out if your prime tower is disabled.
Option found in left side menu under Other (hidden when prime tower disabled), or when right clicking in Flush Options (greyed when prime tower disabled).
Per my reply to post on BambuLab forums: https://forum.bambulab.com/t/help-needed-for-multicolor/56659/12?u=jasoryeh
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