05-20-10: Downunder
I have a Phantom and A90 and I know the problem you are experiencing. I also use the mint tractor. The phantom is wide but not very deep, so it is impossible for all 3 ridges to be in contact with the headshell, only the front ridge.
That's what I have found - the same was true of the Ortofon Jubilee in the Phantom (or the Graham 1.5T for that matter).
05-20-10: Downunder
Your alignment does not sound quite right. The back of the A90 should be parallel. Either both of the back ridges will be seated on the headshell or none will be. Otherwise your cartridge body will be twisted slightly left or right.
I would go through all parts of the alignment again to double check.
Not in my setup with the Phantom II armwand.
Like you say, the Phantom headshell is quite narrow from front to back (narrow oval shape) but at the left-hand rear (looking from the front) there is an asymmetrical extension that connects the headshell back to the wand.
Looking from the front of the cartridge the left rear 'ridge' of the A90 is under the headshell (the extended part that connects back to the wand) - while the right rear 'ridge' does not contact the headshell at all. The cartridge is mounted symmetrically in the headshell and aligned with the Mint protractor (though its in the same position with the Graham jig).
You can clearly see the right rear ridge outside the headshell in this photo
Despite this, the A90 is still by far the best sounding cartridge I've heard in my system. I suspect the rigidity of the cartridge/headshell interface and resonance control etc is still far superior to most other cartridge designs - due to the A90's rigid and highly damped one piece SLM body/spine.