I’m also using the Advanced Locomotion System (ALS) from the marketplace and I had similar issues. It seemed like the only difference between the source and target skeleton were the virtual bones, so I assumed that was issue.
However, it turned out that my animations were retargeting correctly, but the Foot IK was breaking the animation previews. You can disable Foot IK by modifying Mannequin_PostProcess_AnimBP and setting the default for “Enable Foot IK” to be false. This fixed my issue and animations appeared correct afterwards.