I am afraid that it is not clear what is the implementation and the authentication mechanism used for both apps, either the web one and the mobile one.
Could you please elaborate - how are you opening windows and tabs - is it using the InApp Browser? What is the expected correct response? Probably you may want to examine the response of your web site returned to the client app.
Also, you may want to consider using a web service that can verify the user credentials instead of opening your web site and thus authenticating the user into the mobile app.
Let me know if you have questions.
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