it could the garlic and onion being a bit of a shock suddenly being introduced again. Are you having a lot? They can certainly be quite strong and therefore possibly irritating at first. You could experiment for yourself and not have them for some days and see if you get any better. Then start taking them again little by little.
Another possibility is the die off especially since garlic is an antifungal. That is why it would be best if you could keep taking it. Just thinking that if you did not take it for some time and suddenly started again, you may need to build up slowly.
And best to keep the bowels moving; constipation is not helpful for fighting candida.