AFR (Alternating Frame Rate) splits the workload amongst the GPUs by assigning a given frame to each GPU in the CrossFire Chain. So GPU1 renders frame 1 and GPU2 renders frame 2. In theory, you can get double the number of frames because GPU1 can jump straight to frame 3 without working on frame 2. In practice, this is reduced due to CPU overhead and other timing mechanisms which prevent you from always having something to work on.
3D Games are always working on ways to improve frame rate at the same time as providing the best possible visual experience. The easiest way is to re-use data that has already been calculated and sitting in memory from the previous frame. So Frame 1 gets rendered fully, but Frame 2 could just render the differences and copy/paste the unchanged data from frame 1. This causes a headache for MGPU configurations because the data from Frame 1 is not on the same GPU that is rendering Frame 2. If you don't do the copy (and the game has no idea that it has to do so), you end up with flickering issues because Frame 2 is lacking the information in Frame 1. Since it is the GPU driver which is running CF, it needs to detect that a resource is missing and do a copy from the memory of GPU1 to GPU2. This takes time because the path and latency across the PCI-E Bus or CF Interconnects are much greater than between a given GPU and its own onboard memory. The more resources that need to be copied, the longer it takes for Frame 2 to finish and get presented after Frame 1.
Certain CrossFire profiles will skip the transfers that are unnecessary and in that case Frame 2 finishes very quickly because it has less data to compute than Frame 1. In that case your frame rate jumps! Normal CrossFire Profiles will always have some type of extra transfer for various games, but the AFR Friendly one only has very basic settings so it will probably be faster.