First of all, thank you for replying and taking the time to type the life story of the problem for me. If you can send on the pics for me to view that would be brilliant but I will give you advice anyway and once i look at the pics i can give you more.
My god. Where do I start really. There is a lot of conflicting information there.
Firstly. Why didn't they do a pessure test the first time when they said that the water pump was leaking and if they did do one to find the leak that they said was coming from the water pump, why didn't they do one afterwards to check that the system was in fact good again. If they had of then they would've noticed the leak from the manifold at the time. In saying that though, maybe the manifold wasn't leaking the first time and beacause of pressure build up it then caused the leak in the manifold but it is difficult to say now after the fact.
On the issue of the expansion bottle and the brown staining, i would say that you would've seen the hard stain on the bottle yourself if it was there when you were topping up the level yourself and also they would've noticed it also if it is from the bag as the service manager is now saying ( although he said at first that it wasn't). In my experience a reddish brown residue in the coolant system would either be from rust entering into the system or more likely radweld or the likes that will stain everything but rust will occur when you run the system without antifreeze in it by having a major leak that you just keep on topping up with water. So in summary, i don't believe that that is your expansion bottle. I wonder though, most plastic items in cars have a stamp into the actual moulding that has the date that the part was made and you could compare this to another plastic part on the car and see if the dates are close by ( within a month or 2 really) if they are very different then it would seem to me that it is from a different car. The stamp would look like a circle with an arrow on it pointing to a number from 1-12 and either another one next to it with a yr or the yr is stamped into the middle of the first circle.
It is difficult to say what has happened, but i feel you have been mislead by the dealers. I would've done things a lot differently as i don't like fitting parts in the hope of fixing a problem i like to do as much as i can to prove that i have the problem so it is fixed the first time. I'm not saying i'm perfect though, i have got it wrong in the past and i would always hold up my hands and say it. I always believed that if i was honest with my customers and told them everything as i was doing it that even if i got it wrong then they would return as customers because there are a lot of cowboys out there. And also if i did get it wrong i wouldn't charge customers full price for parts that i had fitted if they couldn't be removed or even at all sometimes if i have gotten it really wrong.
Anyway, back on subject.
Before i go on though there is one thing i want to say and that is that if there is pressure build up in the system then the temp will rise. Even if only a bit, but it will rise. Especially if as they say that the impeller isn't circulating the coolant then as the pressure builds up the temp will rise more than normal. You would notice this more when the car is stationary rather than driving as when drivingthe cold air coming through the front of the car will keep the temp down a bit. But still you would notice a difference in the guage. The guage is given its reading from the sensor on the engine block so it is fairly sensitive otherwise why have it there.
I'm sorry if i am flitting about a bit but i am trying to answer every part of your post if i can.
Back on to what i think happened to your car then. I don't think the initial problem was with your water pump and possibly was with your manifold leaking slightly, but as i have said, this is hard to say after the fact. I do think that somehow, air is getting into the heater matrix and airlocking it though. if, as you have said that they have replaced the matrix then the new one should be clear of any debrix and should be able to be cleared of airlocks. If there is a stubborn airlock then you can backfill the system to erradicate this manually and then if the airlock reappears then there is air getting back in to the system from somewhere like a jubilee clip or a connection somewhere. Another pressure test will locate this though.
It is a strange problem though. I do wish the car was in front of me so i could go through things with you step by step and then we could have that eureka moment together.
I am racking my brains thinking of scenarios that would cause your problem and the only thing i keep coming up with is air getting into the system somewhere near to the matrix to let air into the system and airlock the matrix. Under a pressure test though this should show up as a leak. Once the leak is found and tightened then you could backfill the matrix and the rest of the system and the problem should be fixed. The only other way that pressure could be getting into the system if there isn't a leak is through the head as a crack, but this would only usually occur if the engine had overheated badly but can be a manufacturing fault sometimes. But this is very rare.
If i was you i'm afraid i would not go back to the dealer again. I know you have spent a lot of money with them already, but none dealers can sometimes be better than dealerships ( I'm saying this even though i did my apprenticeship at a main dealer where i learnt to be as honest as i can be, which can be my downfall). They should start at the beginning and think of it as a new fault ( if any of the parts that the dealer fitted have to be replaced due to being faulty then they are covered by warranty so don't stress about that). A pressure test needs to be done to elliminate any leaks in the system then go from there to find the cause of air getting into the system or pressure building up and causing the fluid to escape and so causing the air to get into the system.
Again John, I hope i have helped you in this matter. If you have any more questions on this or you just want me to clarify anything please don't hesitate to post back so i can help you more. Unfortunately, i'm in ireland living nowadays so i am not able to drive to you to look at the car myself ( which i would do if i could just to help you more). I will answer any questions you have and give you as much advice as possible on this matter.
Again, if you need help in the future please contact me via my profile and i will be happy to help you again
One last thing but i should've said this at the beginning, thank you for accepting my answer and for the bonus. It is very much appreciated, but my only goal is your happiness with the service i provide you on this site.
Thank you again.