Although the FBV 3 is fully compatible with the POD HD, POD HD Pro, and POD HD Pro X, the footswitch labels do not line up with the corresponding functions as compared to the FBV Shortboard MKII.
The FBV 3 has been redesigned and it no longer has a Function 2 footswitch. What previously was assigned to the Function 2 switch on the Shortboard MKII is now done with FS 1 (Set List Select Mode On/Off) on the FBV3. The footswitches that were labeled Stomp, Modulation, Delay, and Reverb from the Shortboard are now FS 2 - FS 5 on the FBV3. Function 1 (Looper Mode On/Off) remains the same between both pedals.
Also, when assigning stompboxes to footswitches, the POD will not correlate to the FBV 3, it will be off by one. So FS 1 on the Pod corresponds with FS 2 on the FBV3, and FS 2 on the POD is now FS 3, etc. See the figure below for an example.