Reordering layers in web map causes some layer visibility to change in Designer

I created a web map in our Enterprise Portal (version 11.3) that's being used in VertiGIS Studio Web (version 5.29.2) and when I reorder/rearrange the layers on the web map, some layers that are configured to be turned off by default in Web Designer gets reset and visible on the map. When I save the app in Designer, the web map layers reset to what the Designer got reset to. Is anyone running to the same issue?