Ah, that's it. Your clothing base figure loads in Apollos default pose, not in zero pose.
Here's how to fix that:

• load the base;
• choose WIndow->Joint Editor->Zero Figure;
• set all rotations and translations in the Body and the Hip to zero;
• choose Edit->Memorize->FIgure;
• and save back to the library.

Now the clothing base figure will work correctly, and if you apply it to the boots in the setup room, they will conform correctly.

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