I have the same problem after bowel movement. In your case, if it is bad at night, it sounds like a possible enterobius vermicularis infection. [pinworm] I would check as they will be 'just' visible to the naked eye. You will not see the eggs. There is an effective drug for this available at the drug store.
If it is protozoa, I would start on a Black-Walnut -woormwood-clove powder tea. Sip it during the entire day for a week or 2. This should get rid of all sorts of bad stuff. Just be sure to start taking probiotics--or goats yogurt--to rebalance your flora. Shroom