Ok, for a start I made a small mistake - I use ADZs not ADFs since I converted all my ADFs to this format.
Secondly, I think this is a normal operation of the EMU. For some reason after I use an ADZ on Winfellow, it knocks off a kilobyte.
The ADZ continues to work ok however. So it may be the CRC checksum - what is this by the way and why are these ADZs altered under Winfellow and not WinUAE?
I've changed the title of the thread as not to cause panic if this is all that is happening - it's unfair on the authors how I phrased my post title - sorry wasn't thinking.
This EMU is great by the way. Still a little choppy on my 950 Duron with KT266A and DDR, but overall it's great for games.
Great work guys.