EC can manifest in many weird ways. It can affect any organ system that has a high blood supply. The “classic” head tilt is definitely not always present. Not all rabbits present with nystagmus (“tracking), balance issues or hind end weakness, but in those that do, the symptoms can be rather subtle. That EC can affect the kidneys/urinary tract leading to frequent urination and loss of litterbox habits has been well established, but there’s still a lot that’s not fully understood about this parasite.
You could look for another vet perhaps, or you could go for the ec test. EC titres in a symptomatic bun are sometimes (not rarely) very high, which means the rabbit has ec that needs treatment. A positive test is very difficult to argue with even for a vet.
The gold standard treatment is Panacur (fenbendazole) at a dose of 20 mg per kilo body weight and day for 28 days, but its often recommended that the bun is also put on an anti-inflammatory med (meloxicam) to bring down the tissue inflammation the parasite causes. Some vets will also prescribe Pepcid (famotidine) to protect the stomach lining from the meloxicam -this would probably be a good protective measure for a bun that has had GI trouble recently.
For rabbits that for some reason can’t have Panacur (fenbendazole), a med called Ponazuril is sometimes used instead.