You're going to start seeing a lot of problems with the two plants in one party cup. It just simply isn't enough room for each to grow.
I tried growing 2 plants in 1 2-Liter bottle and after the 5th leaf set (about 2 days before I saw sex), the plants started dieing from the lowest leaf set and worked its way up.
If you continue to have problems, make sure you soak the dirt through and through. Then, let it basically completely dry up (right before the plant starts to sag) and then drown them out again. That's how weed likes it in dirt.
Before worrying about PH and other sophisticated junk, usually the problems are much more simple.