Hi Andy,
Thank you so much for your help.
Yes we put a scope on the ISP and RST pins and could see the correct timing.
The board is an old design, we have 3 different designs which were all using the 2368 processor, then we decided to upgrade to the 2387, (2368 and 2387 pin compatiable), The boards ran fine with the new 2387 processor, but then when we wanted to do an upgrade of firmware we couldn't download.
We found that we can download to a fresh processor but after that we can't download, we also found that if we then cleared the processor memory using JTAG we can then download.
We will do some more investigation and let you know if we find anything, if you have any new ideas that would be great.
Thanks