I'm far from being an expert on this subject, but based on what I've read it sounds like avian gastric yeast might actually be fairly widespread, and doesn't cause problems in most birds that have it. There are a number of microbes that are normally present in the body but don't cause problems unless they get out of control, and I wonder if this is one of them.
Once it does get out of control it's hard to cure the problem, and recurrences seem to be pretty common. Stephanie, it's not really clear to me whether the vet gave you an antifungal medication or not (fluconazole aka diflucan). It's best if you have this, but in any case there are natural remedies that may help both now and in the future to help prevent recurrences, and you can give it to the budgies too in case they have anything simmering inside. Not as an everyday thing, but once in a while to help keep the system running smooth and clean. Then afterwards give them yogurt or some other probiotic to help restore any good bacteria that might have been taken out by the anti-microbial stuff.
Looking back through the thread, I noticed that you're giving them thyme. So you've probably seen this source, which says thyme seems to be helpful:
http://www.birds-online.de/gesundheit/g ... gls_en.htm Thyme seems to be generally safe, but it can cause some side effects and I don't know what the safe dose for birds would be.
http://www.healthline.com/natstandardco ... e-thymol#3 So don't go crazy with it, keep the amount fairly small.
Ditto for lemon juice or vinegar, these are acids and it's well known that too much acid is bad. Chili peppers were apparently designed by nature to be eaten by birds, and there are parts of the world where people eat it every day and the population is booming. But still, I'd be careful with it.