Separation is always a good idea, espesially if one is getting bigger and eating more, it's generally the first clue to a dominance issue. 2 females together is just the best pairing, there really isn't a 100% safe one.
Yes, the weather could be slowing them down a bit, but as long as your temps are proper and you're not giving them less UVB/basking hours, 6 months is to young for it to be really impacting them. Babies don't brumate because it's important for them to eat frequently or they won't grow. I'm in WA and it's still snowing here, and my baby's eating as much as ever.
You know if it's parasites by taking a fecal sample to the vet. You can take it to any vet because the tests for parasites are the same for all animals. It varies by vet, but the average price is generally about $25 a sample.