Why is my male dog whining?

As Jojo has asked, is the Rottie female, and not yet spayed? If so, on both counts, then the reason for all this is obvious!!! At 12 months, she should have had her first season by now, but if that happened around 6 months, she could well be coming in again. Or just has been delayed with her first season, which can happen.

Whatever the case, this humping needs to be corrected, obviously, before she gets sick of him and a fight starts. Actually if would be good if she does see him off - usually no amount of me stopping my boys once switched on, worked as well as the b itch herself sorting them out!!!

I think I'd stop the contact for a while - get him out for more exercise. You might have stopped the humping, but the urge is still there = the whining (and even more so IF she's anywhere near coming into season)

Add - Okay, seeing your comment, so he's a castrated male. Well he's NOT going to see your dog off, but he's 'fair game' for your male so again, before this deteriorates, end the playing for a while and concentrate on getting your lad out for more exercise - spend more time with him so he's not frustrated. And please don't necessarily go down the castrating your own dog road because the only certainty with this surgery (and it is an operation with a g/a however 'simple') is no puppies. Castration won't stop the natural urge much as it may lessen it. Castrated males have still been known to mount and even tie with a b itch in season. Another thought - there could be a b itch in season around locally which he's picked up on during a local walk, which has switched him on. If this is the case, the good news is once she's out of season, he should stop all this.

Add 2- Another thought - check the anal glands of the Rottie - sometimes the smell coming from the area is enough to 'interest' other dogs!!!

What Gender is the Rottie?

Ok...The Swiss is just probably dominating the Rottie and/or may be confused about the Rotties Gender as neutered males do not smell the same as intact males.
The Swiss may have become attached to the Rottie or just fascinated with him because he smells neither like a male or a female dog.
Many neutered males get "picked" on by intact males but as both these dogs are still not fully mature it may manifest itself as dominance rather than aggression from the Swiss.
Very common unwanted effect of neutering, especially early neutering, before the neutered dog had gained full sexual maturity and male characteristics, it is called Feminisation syndrome.
Other male dogs are confused and see them as in season bitches.
Also the Rottie may have a uti infection or similar which will induce the Swiss to hump it. Check it out.
Until the dogs are mature I don`t think there is much you can do except correct the humping behaviour or to stop the whining maybe its best to keep them apart for good.
Sorry can`t be of much help.But others may have a better take on this and a practical solution.

You really shouldn't have got two males so close in age and my gut instinct says this is purely dominance from the Swissy as he starts maturing. They would have got on fine until recently as both were pups. They are now both maturing and there lies the problem.

I would advise that you don't neuter the Swissy at the moment to try and keep some distance between them, but treat both to NILIF training and establish more leadership from you.