First of...congratulations! I was asking after you a couple of weeks ago as I hadnt seen you post since asking about whether or not you was going into labour. I guess you had! lol
Have you considered going to disposable nappies for a little while? Unlike towelling nappies, disposables have a layer to help lock moisture in and keep it away from babys delicate skin. What are you using to clean him? Luke warm water and cotton wall may be best if youre using something else. Also, what are you using to help his sore bum? If nothing is helping to make it better, go to your doctor and ask for Timodene (sp?) You only need a tiny amount each time but it works well and more importantly, it works quick! It may have changed now, but when I had it for my first, it was only available on prescription.
I wouldnt think its something you are/arent eating and just down to his little tummy and bowels developing still. I do think you should speak to your health visitor again though for advice as it is still happening. If she still has the same response, ask to see a different one if there is one.