Malamutes are unfortunately one of the breeds that tend to exhibit same sex aggression. I have this issue with my mix and it's why I only introduce her to certain females off leash that I know will submit to her (it's not as much of an issue on neutral territory, but here at/near my house).
I've had a couple of nasty fights between her and my new dog, who is about 14 years old. EVERY time it hasn't been that she suddenly attacked, it has been that the new dog has shown some form of dominance or aggression and elicited the attack. This dog is not generally dominant but in some instances she decides to get "uppity" over something, so to speak, and Morgan feels the need to put her in her place.
I think this is likely the case here. You say your Corgi is submissive, but what are you basing this on? If the Corgi has never had a reason to suspect the other dog is a threat to her position in the pack, she may have just been always relaxed and you're mistaking it for submission. If the malamute has exhibited some behavior that she feels threatens her place in the pack or a possession (the main ones are food (or things related to food like bowls), toys, and space (like sleeping or eating areas)), then she might have shown some body language or behavior that challenged your malamute and caused an attack.
In many cases I see a dog challenge another dog and the dog does not take kindly to it, but the owner thinks the "victim" has been attacked unsolicited and punishes the attacker. In actuality the "victim" is sometimes the instigator and it goes unnoticed. But you need to pay very close attention to what kind of behavior your corgi is exhibiting to elicit an attack and try to curtail that behavior (is she showing guarding behavior over an object? a space? (such as dog bed or sleeping spot). She does not necessarily have to seem aggressive to be doing this. It can be as much as her standing rigid and holding her head up that the malamute sees as a challenge). Did the attacks happen in specific places or situations? (A certain room, during playtime, before a walk, one dog got attention, one dog got let through a doorway first, etc.?). Those are things you can alter to prevent aggression.
I'm kind of worried that you say you're using the Cesar Milan "method". The main reason Cesars methods work for HIM is because he has uncanny timing and can read various body language quickly and accurately. Most people don't have this ability. And people often cite that he keeps a whole pack of dogs with no issues, but this isn't actually the case. I've seen plenty of clips of dogs in his packs getting into fights. He simply knows how to break it up safely, and also has other handlers on hand for help. In any case, he DOES get bitten periodically even then, or his dogs get injuries. Plus the dynamics of a VERY large pack are a bit different than the average home with a few dogs. Trying to follow what he does is nearly impossible for most people, not to mention his shows are extremely edited so some of the things he does go unshown. Also he's not there to assess your individual dog and tell you what tactic he would use. You see him use different methods on different dogs, and not all apply to every dog. Also I've read his original book, and the advice in those tend to be vague and no info for very specific situations. Plus it does mention NOT to alpha roll your dog (which is essentially what you're doing to show dominance) like he would do, and seek expert advice in situations where you have a dog that you think requires such measures. Personally I think alpha rolls are a bit silly (and actually dangerous with truly aggressive dogs), and the average dog tends to see it as a game. I can "alpha roll" my greater swiss mountain dog and she lays there happily knowing she's getting attention.
Also, you mention when the dog attacks you take her to the ground and make her lay. You know what that says to your Corgi? That she's the winner. If she was actually the one eliciting attack through body language you may worsen the situation since she figures she's winning the dispute every time. If anything you should be making BOTH dogs lay down and calm down. You may physically seperate them, but you shouldn't be having to physically take the malamute to the ground. Seperate and give a command to lay down on their sides and relax (the command may be physical through touching/body language, but shouldn't be a case of physically forcing the dog down). You can't FORCE a pecking order and the dogs have to work it out themselves to some extent, so that's why simply punishing one dog in front of the other isn't good.
The other thing is you need to try and stop the aggression before it elevates to physical attack. If you see the corgi showing body language that challenges the malamute over something you need to immediately stop that behavior and seperate them both. If you see the malamute looks to be preparing an attack you need to stop it and seperate them immediately. Once the attack is happening the dogs are in an excited state already, so gaining control and correcting the problem behavior is going to be harder. This may be a bit difficult since you don't seem to be recognizing what behavior is elliciting the attack, or noticing the malamute showing aggressive body language before attack. So you're going to need to supervise at ALL times for the moment and pay very close attention to their behavior and dynamics.
btw I would suggest teaching the "look at me" command if they don't already know it. When you see one dog giving the other dog a little too much negative attention you can use that command and reward for them completing it. Teaching the command will give you a way to get them to focus on you and break their attention from something else when you need to. Obviously teach this first when they're in a relaxed state and slowly work up to more distraction, just like any other command.
There is more than one way to teach this I'm sure, but I personally do it by holding a treat down at my side (at first dogs will focus on the treat) then snapping my fingers in front of my face and saying "lookatme". Immediately when the dogs attention is focused on my eyes I give the treat, and over time work up to them paying attention to you for longer periods.
http://i207.photobucket.com/albums/b...gan/ginger.jpg What three female dogs getting along looks like
. (btw I thought morgan looked kind of like Denali. Her mom was a full blooded malamute. The red one, ginger, is her sister.).