I've noticed that the when using the customized download options released in the Sept 2024 update, all my preferences reset to the default setting every day. For instance, I hide the ability to download shapefiles and reorder the downloadable file types. Everyday it's goes back to the default state.
These are hosted layers that participate in a distributed collaboration and sync every morning. My guess is the sync resets the workspace customization but unsure.
Details on the Hub downloads update which I am using can be found here.
@JohnLivengood please open a case with Esri Support Services to troubleshoot the issue you noted above.