Which BMP085 board do you have? The reason I ask, is that I'm trying to think of what factors could be different between your readings on the Mega and the DigiX. Two possibilities come to mind:
1) The sensor library could have code differences specific to the different processors, that aren't in sync for some reason.
2) The Mega is a 5V board, while the DigiX is 3.3V.
I don't know if the power difference could be a factor or not. But I was noticing that Adafruit's BMP085 sensor seems to be 5V safe, but I know I have a SparkFun sensor that's only for 3.3V. Again, I don't know if your sensor has a regulator, or if there's a mismatch, or if that would cause a problem in any case. It's just something that came to mind.