I’d keep giving the benebac. With probiotics you often have to keep giving it for a prolonged time, in some cases you need really long-term treatment. The good bacteria needs time to establish themselves. In many cases (seen in humans) the good bacteria tend only to survive for a limited time without boosters.
So since you had good results, I’d put her back on Benebac.
If that doesn’t help, you need to investigate further. I just recently found some info about one of the probiotic components in Benebac, enterococcus faecium:
“Eneterococcus faecium (and E faecalis) are Gram-positive bacteria used to control contamination in food, feed and the digestive tract of animals. They are the predominant enterococcal species in the rabbit gut and are able to survive the acidic gastric pH, colonise the mucosal surfaces and prevent the attachment of pathogens (Linaje et al, 2004).”
Here’s whole article: http://www.vettimes.co.uk/article/beneficial-bacteria-in-pet-rabbits/