I switched to non-bio (about a tablespoon per wash) when I started using cloth because we also got a few problems with red bottoms when using bamboo/cotton in contact with skin. However, around the same time I switched to using pockets which all had fleece inners and the problem cleared up.
Recently, i have started using about a tbsp of Ariel for the nappy wash and we have no problems at all. So in hindsight, I think it was just a bit of detergent build up in the bamboo/cotton which gave sore bums when weed on.
I think you might find using a fleece liner helps and I'd make sure you only use a teeny amout of detergent in the wash and do a couple of rinses after the main wash to get rid of any excess detergent (nappies are very absorbant so also take up lots of the detergent in the wash).
PS I used to leave it ages between changes in disposies but have since read that this isn't a good thing to do due to chemicals etc in them. I think even the manufacturers recommend changing disps every 2-3 hours. I change Nells cloth nappies every 3-4 hours (depending how wet they are)