
You need to go back to the vet and have a full faecal examination, including worm count, and tested for giardia (3 faecal samples will be needed for this test), it could possibly be this as it is a protozoa and can be difficult to find. However panacur and also metronidazole will eliminate it. Sometimes it takes a number of treatments especially if your puppy is a scavenger, and when out walking drinks from pond water etc., or eats his own faeces.
It could also be any one of a number of conditions including camplyobacter, you need to keep pestering your vet until the cause is found.