Hi Tina,
I did some research and was able to find this issue being reported a few times in the past but I could not find a solution or confirmation of a bug in the app. The app developers are much more involved with user support these days than they were in the past so I'm confident they will be able to assist resolving your issue.
You can post directly in the app support forums using your wordpress.org login credentials. The Apple IOS support is located at http://ios.forums.wordpress.org/ and the android support is located at http://android.forums.wordpress.org/forum/troubleshooting
Before posting your support topic It might help to test the XMLPRC endpoint for the subdomain installs. You can do that using the xmlrpc validator at http://xmlrpc.eritreo.it/ Just input the url to one of the sub domain blogs
Could you please post a link back here to your support topic, I would like to follow and see how this gets resolved. Thanks.
Here are links to other unresolved reports of similar issues:
http://ios.forums.wordpress.org/topic/compatible-with-sub-directory?replies=4#post-10858
http://ios.forums.wordpress.org/topic/cannot-login?replies=23#post-10333