The FTDI 2232H is an upgraded version of the 2232D. The protocol seems the same, the big differences is in the power supply since the H version is a modern 1.8V design. I don't know about Papilio since I wrote my own loader. I am using the 2232H with a spartan 6 9K I used port B for programing and port A for a Async/Sync FiFo. Some things to note. 1. When port A goes into full sync mode you can't access Port B, But port B will stay in the state it was in. I used BD4 for reset I am not sure what pins Papilio wants. 2. The full sycnronous mode has a glitch on the TXE line where it will go low even if it can't receive a byte. You have to check the line at the end of the cycle to see if it accepted the byte. 3. If you use a DCM or PLL lock signal to switch between Async and Sync mode you will have to leave the WR line high in Async mode and just rely on the falling edge. It seems to work fine this way.