Following on from my post re 'after kennel cough' It would seem this is not kennel cough. I have noticed that she only coughs when she is laying down such as all through the night. When she gets up there is no coughing all day. With the antibiotics etc she is happier in herself and willing to run with the other dogs, although she does go back to bed after this as though she is a bit washed out. But no coughing at all, then at night when she goes to bed it starts around 2am and continues until she gets up in the morning.
I have checked to see if there is anything that could set this off, but no air fresheners and as the other dogs don't like the sound that comes from her, they prefer to sleep in the lounge, so this means she has a choice of 3 beds to sleep in.
When I first got her she had a slight bald area underneath her throat as though she may have been tied up with a rope ( I am guessing as she was abandoned) and wondered if this could have damaged her throat which may cause her a problem when she lays down.
She will go back to the vet on Monday, possibly for an X-ray, but wondered if anyone had any ideas about her problem

She may have had kennel cough when I first got her, but this improved rapidly and she had one week completely clear of coughing until it came back with a force roughly a week ago and the infection was found, but it is not improving with medication yet. ( also none of the other dogs have caught the KC if that was what it was )

Don't know if it's relevant here, but one of the signs of asthma is coughing at night - in the wee small hours.     It's the most common sign in children, who often don't wheeze, but cough instead.

Hope you find out what's going on soon.

I'd get her back to the vets and get her heart and lungs checked out, an early appointment as close to her waking up as possible.

it could very well be the Lungworm, I'd wait and see how she is after the full course of treatment, both antiparasite and antibiotics..

Respiratory problems can be exacerbated by laying down.  Fluid will pool, and become irritating, and dust can be a factor too as your dog will be inhaling air very near to carpets, fleece etc

... think about how people often cough more at night, in bed, or when tired

It could also be the result of a physical issue - for instance I have a dog with only one lung and he certainly finds it more difficult to breathe if he lays on one particular side, even without the added complication of kennel cough - so you might be right to consider other causes such as throat/neck damage.  

Whilst you and you vet investigate other options make sure your girls bedding is washed with low allergy washing liquid such as Surcare or perhaps no soap at all.  I know that some washing scents make my cough worse if I have a chest infection.  Also remove fluffy bedding and replace it with cotton towelling or smooth cotton sheets to minimise dust.  Check with your vet about cough liquid - I know that many vets suggest Benylin for kennel cough - as it can be soothing for a sore throat. If he doesn't want to prescribe medicine then you can make a soothing liquid with honey and hot water which might help her if given last thing at night.  Finally keep her exercise to a minimum for a while and keep her indoors when it's very hot and dusty outside.  Hopefully it will only be a short time before you see some improvement. 

Fingers crossed you get answers soon x

Update.
She was taken in this morning for examination and X-ray under anaesthetic. My vet was horrified to find so much pus in her throat, so this confirms a massive infection. Swabs have been sent off to find out exactly the type of infection so that it is treated correctly, but as this is by a grown culture it can take a little while to get the answers back. Also she showed me the X-rays and she has thickening of the lungs and a couple of darker patches,, so it looks as though this has been untreated for quite some time. Her lymph nodes are up throughout her body so I thought of cancer, but my vet doesn't think it is this, she thinks it is caused by the infection, and still has not discounted lung worm, so this treatment continues along with the anti inflammatories.
If we get no improvement with the Panacur for the lungworm then she may have to do a biopsy of the lymph glands

Poor little soul, as if she hasn't been through enough

Positive thoughts going out to the poor wee soul.

Oh poor sweet girl.  How brave she has been carrying on and doing her best.  Hope she makes a full recovery now though.  At least being a beagle she should not be too difficult to get the treatment into her.