Hi Joe, I just downloaded the latest changes and did a full rebuild and deploy from source, but I still had the issue. I debugged and was able to fix it by commenting out the following statement in EnsureItems() in skinSettings.ascx.cs:
if ((dd.Items.Count > 0)&&(!catalogChanged)) { return; }
It seems that catalogChanged is not being updated reliably when selecting a new site. Hope that helps.
Jamie