Hey Paul. You should look at the Proton+ routines on the GHI website. They gave me some excellent insight into timing that the GHI docs were sadly lacking in. After powering up the board, do a hard reset by bringing the reset pin to gnd, then let it float by making the associated pin an input. Do not use weak pullups on portB at this point. The reset routine for proton is what I followed. Next, if all is well, you should see a "BL". This will tell you the bootloader is ready to either load the Alfat firmware, or update it. At this point send "R" or "RS" ? Check the Alfat docs on this. You should get the Alfat startup message complete with version number. If you get this far, you're 3/4 of the way there....
Ron