I actually just made one of those a couple weeks ago, just in a different plastic case. Super useful and cheap project. However I found that it gets balance issues when you have only one channel quiet or silent... the other side gets much louder. Could be the size of resistors I used (1k), I don't really know how to fix it.
Does that happen with yours?
Shintarou,
I am trying re-create your scenario and I am not experiencing any balance issues.
The only time I am experiencing anything you are explaining is that if I have multiple inputs plugged in, i.e. if I only have one gameboy plugged in, it is "louder" than if I had two plugged in, but that is a trade-off of utilizing passive mixers.
Were all your solder connections solid and did you test for resistance at the jack and wires after you were done with making your mixer?
***edit***
Shintarou,
The drop in signal is more pronounced when plugging in directly to the headphone jack of a gameboy. There is noticeably less drop in signal when plugged into a prosound jack of a gameboy.