It could be some sort of noise problem, however it certainly didn't exist when I used this circuit with the arduino, (at 5V, so maybe S/N ratio was small enough or the arduino just has more hysteresis).
I think the version of Energia code I'm using may have a bug:
I decided to break the circuit up and have one phototransistor trigger the rising edge interrupt pin and one phototransistor trigger the falling edge interrupt pin. I've noticed that they both end up triggering their respective interrupts when I remove my finger from their light beam-- it seems that they are both triggering on the falling edge for some reason, even though I specified rising for one of them in the code.
I think I read something about rising not working somewhere, I'm going to see if I can find out where I read it.
The problem was a bug in the library Energia.h. It specifies the wrong values for RISING and FALLING. The solution was already discussed here: (See post #6)