I would strongly suggest you read that article I suggested. That and more is explained.

Notice the wide range of voltages each LED has? That is because they truly aren't that predictable, each LED can drop its own unique voltage, leaving the other starving for sufficient voltage to turn on. LEDs from the same die during manufacturing are more likely to be similar, which is why you got by with it, but it is not a given.

I get the feeling you are using a 9V battery. 9V batteries usually drop to 7V quite quickly, and stay there until they are discharged. There are electronic ways to get around this, but most of us like simplicity.

 

Why is wiring them in parallel not recommended? I've been doing this with almost all my single color setups :/

Read about current hogging in this link http://en.wikipedia.org/wiki/Thermal_runaway

 

Why is wiring them in parallel not recommended? I've been doing this with almost all my single color setups :/

He said "directly in parallel. The figure to the left is wired with two LEDs directly in parallel. The one on the right shows the LEDs as part of a leg. Each LED or string of LEDs in parallel with others needs its own resistor.