I tried about 10 loaves with slight variations in the recipe before I finally had success. The answer was to ignore the manual. The manual says use program 3 for wholemeal bread. This heats the ingredients for 30 mins which it says is required for wholemeal flower. I found that during this 30 mins, the yeast was proving. This meant that the bread rose too early and was sunk before it finished cooking. I now use the program 1 setting. It appears wholemeal flower doesn't need the 30 mins at all. My bread rises fine now.