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I’m sure the LSM303 could be integrated into ModularSensors. You should also be able to use it along with ModularSensors without actually integrating it. You might not be able to use the “logData” function though – you might have to break it up some.
So, do you have your program somewhere I could look at? Are you turning off the power to the sensor between reading? (Is your I2C port set to switched power?) Are you sure the sensor is powered when you’re trying to read it? Did you try putting a begin() for the LSM303 right before it’s read? In that library it looks like the begin() function sends an activate command which it may need after every power up (or even after every time I2C is disconnected).