I understand that you were able to use I2C with your breakout board, so check that you are using the same level translators, pull-up resistors and check that the Edison is detecting the I2C device on your custom board. But from what you're telling me, it looks like this issue might be related to your custom board.
The problem was indeed in level translator. As I learned the hard way not every level translator can be used for I2C communication.
It looks like you may be using an older build as well. There were several I2C improvements in the last software release (release 2) that you'll probably want to take advantage of if not doing so already.