I have the same problem on my Iphone 4s. I wrote to them and describe my problem and this is what they say:
Hello Marcin - we have heard reports of a few people experiencing this problem, but our customer support technicians have never been able to reproduce the issue and determine a fix. Would you mind opening a free support ticket and discussing the problem with our support team? They are very interested in helping you resolve the problem and they would love to hear more about how your phone is set up so we can duplicate the issue here. You can open a free support ticket on our website: http://line6.com/support/tickets/add.html Thank you!
In my opinion they will not update mobile pod soon because as far i know it work fine with Sonic Port....