Weird clicking sound, part 2.

Question
<<Is the sound coming from his mouth? When does he do it? Does he do it when your petting him or when he is sitting there in his little house or bed and seems calm and quiet?

Have you ever heard of "bruxing?"   
I have a feeling that is what you are hearing.  Rats grind their teeth together very very fast during rest or when they are really happy and content. This is one of the ways rats keep their teeth worn down to the proper levels. Sometimes when they brux, the forceful vibrations cause the muscles from the eyeballs to make the eyes also vibrate real fast making the eyes appear like they are going to bobble right out of their sockets. This is called "Boggling" and often when you hear a rat brux, you can watch carefully and see the eyes boggle too.  Its all really cute.  I went on a search at youtube.com and typed in the search box:
"Rat bruxing" and you can hear and see what it sounds like to compare it to what you are hearing.  

Let me know if you do this.  Even so, let me know if the sound is indeed coming from the rats mouth and what is the rat doing at the times you hear this clicking sound?

I do think  that it is indeed bruxing you are hearing and it is totally normal. In fact, most of the time a  rat is content and happy when they brux so its a good thing:)>>

I'm pretty sure it's not bruxing. I'm more convinced, after today, that it's some type of congestion in his nose. The sound resembles static, the more I hear it. It's not coming from his chest. It's more from his mouth/nose area. He doesn't do it all the time, but seems to do it when excited/agitated (hungry, playing). He doesn't do it when sleeping, as far as I know. That's what is confusing. I would think that he would make the noise, if congestion, every time he breathes. He doesn't. After giving him the baytril for the 10 days, it seemed to have stopped. A couple weeks later, it's back again. The noise was really loud this morning. I could hear it 20 feet away. Once I fed him, it stopped.  

Answer
Thanks- that clears things up a bit more for me.

You just showed me that he indeed has mycoplasmosis and here is why:

Myco of course is found in the mucus membranes and the lining of the nose is a perfect host.
Baytril it the best drug for this relentless organism because it lacks a cell wall. This evil eveil bacteria lacks a cell wall which in turn means that there is not a huge line of antibiotics that are able to destroy it. However, baytril and the entire line of broad-spectrum fluoroquinolone agents including cipro, a second generation fluoroquinolone, are able to fight off bacteria head on, instead of attacking the cell wall. The problem with baytril in general is that they are not the best choice to fight most streptococci, which is why I like to use another antibiotic along with baytril if they seem to relapse fast. I have had success with cefa drops or keflex.

However,in this particular case, I see the problem is that your rat was not given the baytril long enough. WHen dealing with a normal infection, 7 to 10 days is usually the normal protocol. When dealing with mycoplasmosis, however, this bacteria is stubborn and as you know it never really goes away. It can be held at bay, but its always there, lingering.  Because of this, relapse is a serious problem and the main reason it is so serious is because the second attack is worse than the first. By this time the rat may have a weaker immune system since it was trying to fight off the mycoplasma bacteria.
The best way to deal with this is to treat the rat for a full 30 days. Some vets may opt for 21 days at the most, but if you see satisfactory results in the first  3 days and the rat is slowly improving, a duration of 30 days is really the best way to treat myco. As I said before, a secondary infection may be right behind, possibly pneumonia, and this is when the damage starts such as lung scarring or even abscesss.
I would put him back on the baytril now while it is just in his nasal passages and continue for the next 21 days since he already had it for 10 days thus far UNLESS you say that the time he was on it up until  now has been several weeks, which in turn means he should start all over again at ground zero.

You can read up more on my site about myco. I have done alot of research as well as worked with various vets in trying to establish the best route to take  (chemically) when dealing with myco. Although we  cant stop it completely (that would be wonderful!!) there are a few things that can be done to contain it.