Web Apps reversing Web Map Layers

[HaroldKrivell]

One of our customers are experiencing a strange glitch when building Web Apps using WebApp Builder. When the customer links the web map with her web app, the web app reverses the order of her layers and the polygons are on top of the points. We have tried multiple methods to fix this, including...

-Hosting all layers on the portal
-Referencing layers from a database
-Creating separate map services for each layer
-All layers are feature Layers

All results are reversed map layer orders when used by web app. If anybody has a solution for this problem or know why this is happening, that would be great.