In order for this solution to make sense more info is needed: Using MVC5, with WebAPI 2.0, and the OData nuget package version 5.0
For some reason JayData is trying to use OData v2. So to fix it, I dug through the source code and found that you can specify V3.
Change the configuration of your context to include maxDataServiceVersion: "3.0".
From this:
dbContext = new MyEntities({ name: 'oData', oDataServiceHost: '/odata' }));
To this:
dbContext = new MyEntities({ name: 'oData', oDataServiceHost: '/odata', maxDataServiceVersion: '3.0' }));
And that works for me.
It would be nice if JayStack would document the configuration options available.