Well I seem to have solved my problem.

After extensively trying every fix I could find in the forum I did the following and everything downloaded fine.

1. Reinstalled firmware (latest) and disconnected pronto.
2. Opened up PENG (latest) and my latest PCF and attempted to download.
3. "The CF version is not correct or the memory is corrupt"
4. Without disconnecting I tried to upload from the pronto which gave me an uploading error (don't have the exact wording from the screen, sorry)
5. Without disconnecting again or closing down PCF downloaded to the Pronto.

Low and behold it downloaded fine.

Hope this helps someone.