There are different types of colonics and some are more effective than others. Provided the equipment was disposable or properly sterilized and appropriate sanitation practices were used, it is unlikely that you experienced any contamination. As Spirit pointed out, you may be lacking in beneficial bacteria...as a great many people are.
It sounds like you had a better experience with the first type of colonic you had...perhaps you might want to return there for your colonics or locate another facility that has the same type of equipment.
If you know the types of equipment and procedures that were used for each colonic, I may be able to assist you further.