Hi,
i'm a Flash developer and i had the same issue. Today I tried something i saw on another site, it's to change the XML descriptor and put :
<InfoAdditions><![CDATA[
<key>UIDeviceFamily</key>
<array>
<string>1</string>
<string>2</string>
</array>
<key>MinimumOSVersion</key>
<string>6.1</string>
]]></InfoAdditions>
It seems that the "MinimumOSVersion" option works, i tried with 6.0 and had the same error, but now with 6.1 I don't have any error.. well i cross my fingers.
Hope it helps.