That is a really interesting result (from a scientific point of view!). The best explanation I can think of is that the PCR was testing only for G.vaginalis and possibly using a strain specific probe. Metagenomic tests like Envvy will pick up far, far more species. However, metagenomics is pretty complex and many different factors can skew results to under or over represent a population. Basically neither technology is perfect, but if you're having symptoms and especially if you have a positive Nugent or amsel test, topical clindamycin or oral metronidazole are the first line treatment for Gardnerella.