Considered posting in an older topic about this, but my theory is different from the main ones in the Compendium FAQ, so I figured I'd start fresh.
First off, this theory assumes that the Dreamstones are capable of holding their "proper charge"* for a long time, second, we assume Dreamstones "attract" energy, and thus is why they were used at all.
The Masamune (Ruby Knife, Dreamstone) drain energy from eachother due to diffusion(object with greater energy disperses its energy into object with lesser energy until both are equal, or relatively equal by percentage...Not a new concept). The Ruby Knife was designed to take energy from the Mammon Machine, however, as the Knife, it wasn't capable of handling enough power to be useful, thus Masa and Mune 'awakened', becoming the Masamune. The sword, having more theoretical capacity (whether it be physical or metaphysical capacity, IE physical size or spiritual powers) was able to siphon off considerable amounts of energy from the Dreamstone inside the Mammon Machine.
(Melchior used his Dream companions as the catalyst for the Ruby Knife, knowing that the capacity of the Dreamstone in the knife alone wouldn't be enough to drain the Machine)
So, the Mammon Machine, having greater stores of energy, diffused that power into the competely uncharged Masamune. (like an air freshener dispersing throughout a room instead of staying directly where it was sprayed)
That explains the Mammon Machine, but why does it work on Magus? Several theories have been proposed, and one seemed to be getting close, but it went the wrong direction in my opinion.
Before I continue, lets remember something Schala said to Janus...
(lacking an actual quote, I'll give the gist of the scene) Schala gives Janus 'a magical amulet that will protect you'
as she effectively describes it. This amulet, is in fact the same type of amulet that allows interface with the Mammon Machine.
NOTE: These amulets were imbued with Dreamstone also.
Janus keeps this amulet all the way up to the point at which you are given the choice to recruit or kill him(as Magus).
Should you choose to recruit him or not, you obtain his amulet, which was drained of its power at some point previous. However, when you fight him the first time, in 600AD, the amulet still has power(This is where the theory effectively starts). The Masamune, having been most likely unused(as a Dreamstone object, unused that is) for thousands of years, broken, and finally reforged using a new piece of Dreamstone, lost its energy charge(that it had gained from the Mammon Machine)
Now to the point, Magus' magic defense was partly a side effect of the amulet's power (which Schala had given the protective magic). The amulet may not have been fully charged** by the time 'we' fight Magus in 600AD. During this fight, (if used... though I don't see why it wouldn't be) the Masamune drains energy-- not from Magus himself, but from the amulet's protective charm. The same can be true of the next bout, if 'we' choose to kill Magus.
Now, having said all of this, you probably think to yourself:
Question: Then why does the amulet not work on the sealed doors if it still has some charge?
Answer: Simple, the amulet in Magus' possession was A. not fully charged anyway, due to time, B. It was storing an energy it wasn't designed to store, and thus it sped the loss of energy, and C. the doors weren't meant to open with just any type of energy, such as the energy of the protective charm, but specifically the Lavos energy.
Q: Why, then, does the Masamune drain the protective charm from the amulet?
A: Because, the energy in the amulet was only barely being held inside it in the first place, the force of 2 Dreamstone artifacts vying for the energy would still lead to the dispersal of the energy. Not to mention the Masamune was designed to drained the Mammon Machine itself, so the capacity to drain an already diminishing protective charm would be more than easy...
Q: Why doesn't the Masamune have the same protective powers as the amulet did, if it drained the amulet's power?
A: While the Masamune did draw the energy away from the Amulet, it was not made to harness the protective energy, and thus, did not store it. Schala specifically and purposely charged the amulet herself. No one attempted to "trap" the protect charm in the Masamune.
*Energy harvested from the Mammon Machine's interface with Lavos.
**(possible due to the fact that the magical energy Schala charged it with was likely not the intended type of energy, and Magus did have it for a few good years)
Now, have I forgotten anything? what do you all think? Is my observation of things in some way faulty, it seems rather sound in my mind... (though maybe a little confusing to read... I'm not sure about that...)