Does it sound like really loud sniffing? When they're trying to smell something they can sniff really loud and really fast. Could also be sneezing. Is there anything new she could be smelling that might make her sneeze?

 

It doesn't sound like sniffling, it sounds like really weird repeated sneezing, it's through her nose, she does it a whole bunch of times before she stops, she never does just one, she also does it really fast and about every 5 minutes she does it, except when she is asleep, she especially does it when I hold her, or right after I put her back in her cage, and no, I don't believe there is anything new that she could be smelling that makes her sneeze...

 

Could it be hiccups? Rats hiccup quite a lot especially after waking up. They also chatter when they are excited or scared. It's sort of sounds like a quick chuffing sound.

 

The noises you are explaining sound like a respiratory infection. Any excessive porphyrin? Congestion? Snotty sneezes? Labored breathing/ deep breathing?

 

Well, sometimes when I'm looking at Missy, she sneezes and it gets all over my face (I wash it off though), so yeah, I'd say she has snotty sneezes. I don't thing she has any of the rest of the stuff you listed...

 

Sounds respiratory to me as well. Nibbles doesn't do it as much but Jesse gets soft sneezing fits every 5-10 minutes when he's got a URI. If she twitches or jumps during the fits it's even more likely.

it's kind of like a sneeze, but through her nose

Isn't a rat sneeze usually through the nose? Does she make a completely different sound at times you know are sneezes? It would really help if you could record a video and put it on YouTube.

 

Are you going to see a vet? Any videos of her making the sound?