There can be multiple reasons for this behaviour. If your avatar happened to have write defaults on your toggles, you will need to follow this documentation to fix your toggles and other related animations: https://docs.google.com/document/d/1LBzv1jzLN7PlTPxDH1KtQ7TnJZ8O_s76F6yQESkpf00/
If you didn’t receive a message, there is a possibility that your toggles/transforms are outside of the FX layer, which will not be taken in charge when the STT applies its automated fix on all FX animations/motions. (Gesture layer = shapekey modification only)
If you have transform manipulation or toggles on any controller but the FX controller, you need to copy those layers onto the FX controller. If you have shapekey stuff AND transform stuff in the animations, just move those onto the FX controller as well.
Everything should work up to this point, although if you want to follow the VRC documentation, it is preferable to split those animations and apply them separately. The copied layers should go above the STT stuff. Most of the time it won’t need to, but it’s better to be safe than sorry.