This is what I call a Vxml Server 'hung' license and shouldn't really 'ever' occur. It indicates a bug in the gateway or Vxml Server, or in the communication between them.
a) There's a bad version of the gateway software C3900e-UNIVERSALK9-M), Version 15.2(4)M5, RELEASE SOFTWARE (fc2). causing bug # CSCul03432.
Are you using that version on the vxml gateway? If so, you should switch.
b) If not, then you should look in the application logs to find the Session ID for the calls that display Session Timeout. And perhaps post that portion of the log for a few calls. Also see if there's an error log with that same Session ID. The Session ID is the number at the beginning of each line in the Activity Log.