My X10 system is now working again following the help of the Pronto Development Team and Dave Houston - many thanks to both of them.
The problem was solved by changing the way in which I accessed the codes. Previously I used a number of links to join a map of my lighting system to a series of buttons for ON/OFF/DIM/BRIGHT which then linked to a further page which contained the relevant codes. I now have the codes pasted directly onto the buttons and have also removed an in-built delay (as I used to execute a macro consisting of, say, A1 ON - DELAY 0.5 - A1 DIM). I think the macro delay timing caused the problem, and this was somehow affected by the change in the Pronto's firmware. It was only my DIM/BRIGHT commands that were affected, my ON/OFF commands still worked, and it was only the DIM/BRIGHT commands that included the time-delay macro.
So if you remove the macro and paste the DIM/BRIGHT commands under the buttons they should still work. (Though it does mean that if you want to change the lighting intensity fo a specific X10 light you will have to manually select it first and then DIM/BRIGHT). A longer delay time in the macro might work though I haven't checked this yet. The normal codes generated (in my case by using Dave Houston's excellent CodeGen program) should still work.
Once again my thanks to Dave and the Pronto Development Team - the latter who have restored my faith in Phillips!