Maybe it's just your body's way of adjusting to a new way of eating and, if you stick with it, it will settle down on its own. Or is there anything that you've started to eat a lot of that you didn't eat before? For eg wholemeal bread (rather than white) lots of fruit, veg, yoghurts etc? Maybe have a look back at your food diary to spot the changes and match it with the times you've had (ahem) "trouble".