Hi Martin,
Yes, the change from 2.0.1 to 2.1.0 was rather dramatic in its shift away from a dependency on the Mobile Access server. Alas, there is no migration path for upgrading. However, having read your question, I have a few bits of info to offer that might help address the issues you're experiencing.
You can use Splunk Mobile App independently to access your Splunk platform; you do not have to use Splunk Add-on for Mobile Access in. That said, if your end users use the app and you haven't installed the add-on, your Splunk platform instance must use the following ports: Splunk management port: 8089 Splunk web port: 8000. If it doesn't use those default ports, the end user must specify the Splunk web port your Splunk platform uses when they log in to the app. See Step 3 on http://docs.splunk.com/Documentation/MobileApp/2.1.0/Install/Login
It sounds like you have deployed the add-on on your Splunk instance-- is that so? If end users of the app are accessing Splunk through a DMZ, they need to enter both the port and the path of your Splunk web to be able to log in.
Hope that helps-- do message back with more specifics if I'm on the wrong track.
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