I have a 4 year old entire bitch who lives with an entire male and neutered male. She and my other bitch (who has since passed away) regularly used to hump each other. The bitch I have now is a very dominant bitch but would happily take turns with my other bitch at humping (both were entire).It was particularly noticeable when one of them was coming into season or was in season.

Lately I have noticed my bitch trying to hump my neutered male, he is very submissive and will lie on the floor in front of her if she try's to play but she keeps taking this opportunity to try and hump him. He isn't happy about it and growls at her which generally causes a scuffle between them. She is due a season any time now and this has only been going on for a week or so. My question is, do you think she will stop harassing him once her season is done?

She takes absolutely no notice whatsoever of my entire male.

neutered males give off different pheremones, due to hormonal change.If you are mating her she may stop trying to court your neutered boy.Neutered males can obviously still mate (if he wanted to ) still damage a bitch , if pulling away etc . but don't produce pups . Depends a lot on the age the dog was neutered too.

He was neutered before we got him but I'm fairly sure he it was over 18 months old. She isn't going to be mated. He has had form for trying to mate (but with the other bitch i had) but he has never tried it on with this one before, to be honest I think she terrifies him!

Ill keep an eye on them and once her season starts ill separate them as I do with my entire male.

My my fourteen month old bitch is just in her second season and is acting similar with our younger female pup who is nearly four months old she tries to hump her head poor puppy

Although bitches tend to act like this during seasons, I would be worried as she, not only is used to behaving this way with the other bitch, but is not yet in season.  My old bitch does this but only when nearing her day, (like she would start on day 8 of her season) and then stops within a few days or once mated. I take it as a practise session!!lol. 
This sounds more like behavioural rather than season and she could just be pushing home the fact that he is beneath her in the old pecking order.  If she is a habitual humper, I would stop it now rather than let it become habit with this dog, especially as he has issues with this and it causes a scuffle.  My entire male was a humper(excitement not dominance) but he had to be trained out of this behaviour as he was really uspetting the old girl with his nonsense.  I just kept a leash on him when he was in the house and as soon as he got too excited and started the humping, I would take the leash and say 'No' in my tough voice then lead him outside(as he sometimes could'nt stop and would air-hump till he 'finished')(gross!).  Once he calmed down, I would bring him back in but if he started to play the same way, I would just lead him outside again.  He soon learned and now I just need to say 'No' and he stops straight away.

My female (T-Bone) soon to be 11 yrs next month was spayed at 5 months and she humps the puppy :-( I figured it
was a dominance thing, but have told her to stop...

I think you're probably partly right with the dominance thing for my girl as she is a Dominant alpha female, but thankfully it's only started since she came into season, last season she only had her beds to hump and she did this for quite a while after her season finished.