That makes no sense. All the Align Weapon spell is doing is giving the weapon an alignment. That's it. the Black blade already HAS an alignment, and so should function exactly as it would if the alignment came from the Align Weapon spell.
Let's take Bull's Strength. It adds +4 STR to the target. So a thing with a base 16 STR, is now identical to another thing with 20 STR. The spell simply adds something to one, which the other already posses making them equal.
All Align weapon does is take an existing weapon, and add an alignment, which then allows it to bypass DR. The black blade already has the alignment attached to it the exact same as if it had the spell cast on it and so should function the exact same way. just like a person with 16 Base STR and Bull's Strength, functions the same as someone with a base 20 STR.
From the spell itself
" A weapon that is aligned can bypass the damage reduction of certain creatures"
And the Black Blade IS aligned, just through means different then the spell but with the same result.