A quick fix
In reviewing the AIF Service generation classes between RTM CU5 + Feature Pack and R3, I found a small difference in the AifServiceDataTypeGenerator class.
Specifically the method highlighted in the image above, the generateDataContractClass. Previously, we had been able to deploy AIF ports that used Data Contract Classes which extend SysOperationDataContractBase. In AX 2012 R3, this was broken - for details see my previous post.