< Very odd behavior and I suspect buggy programming >

I repeated your experiment and examined the project folder and there's no bugs or odd behavior. There's an explanation for the wacky results that seem inconsistent or not understandable. I'll post some screenshots to help explain and also make some suggestions that differ a bit from your workflow and the reasoning for these suggestions.

First. The import audio function predates the Stems Splitter feature and the BIAB program has use for both functions. They have different processes and use from each other.

Only the Audio Channel has unique capability for audio. Meaning, BIAB exclusively uses the Audio Channel with the Audio Chord Wizard (ACW). The Stems Splitter also exclusively uses the Audio Channel with the Audio Chord Wizard (ACW). Selecting any track other than the Audio Track and activating the Audio Chord Wizard and the screen will jump to the Audio Track.

The bottom line, to use the ACW with the Stems Splitter, the audio has to be loaded or copied onto the Audio Channel. This is the default for the Stems Splitter and the ACW.

The second factor that can be confusing is how the audio stems integrate with the BIAB program. Orange audio tracks are proprietary to the BIAB flagship program. These are called Artist Performance Files. They have multiple purposes and functions with both editing, residing on Mixer tracks other than the Audio Channel, and with the Stems Splitter. When using the Stems Splitter, the stems are both split and processed by the Stems Splitter so they can reside as audio on the 23 other tracks of the BIAB Mixer.

As you found, the named instrument tracks are the backup tracks and the numbered tracks are the Utility Tracks used by the Stems Splitter.

My suggestion is to use the default settings of the Stems Splitter in order to always have consistent and predictable results. Importing to the audio track is intended more for projects that utilize audio but it's not necessary for the Stems Splitter.

Attached Files (Click to download or enlarge) (Only available when you are logged in)
Stems Splitter opened with Defaults.jpg (178.55 KB, 42 downloads)
Stems Loaded Onto Utility Tracks #1-#5.jpg (132.72 KB, 42 downloads)
Project Folder.jpg (51.23 KB, 42 downloads)
Project Folder Preserved.jpg (55.66 KB, 42 downloads)
BIAB 2025:RB 2025, Latest builds: Dell Optiplex 7040 Desktop; Windows-10-64 bit, Intel Core i7-6700 3.4GHz CPU and 16 GB Ram Memory.