If you are responding to Flagyl then it is a good possibility that you are dealing with either protozoa or rogue bacteria. Typically Flagyl is not enough to get rid of protozoa but is more effective towards bacteria as a sole therapy.
Testing is very hit or miss however the best test done for many is the MetaMetrix GI Effects test (use panel #2105). If you do this test and find protozoa, I have an outside forum at http://pptu.lefora.com
which has loads of educational material.