Generally speaking (I am not familiar with the SalesForce mobile developer), if you use the SDK correctly (it seemed difficult to use it, only it did not support the latest versions of Cordoba?), It should support the application. This indicates that the problem is with SalesForce settings.
Inside SalesForce, go to
Setup | Administration Setup | Manage Apps | Connected Apps
and look
Require Users to Log In
option. Is it set up so that users only have to register when they first use the application, and permissions are supported?
If this does not help, try the settings described here here, especially part of the update token.
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