I've had a similar issue to you.
We access the ADXL345 through I2C:
Code:
i2c = DigitalModule.getInstance(2).getI2C(slot);
Every time we try to read the ADXL345, we get this output:
[frcrun] [cRIO] Digital module 2 is not present.
[frcrun] [cRIO] DIO LoopTiming: 260, expecting: 261
We've updated the cRIO to the 2012 image, and updated the frc netbeans libraries.
I was looking through SensorBase, and this javadoc on SensorBase.checkDigitalModule() looked interesting:
Module numbers are 1 or 2 (they are no longer real cRIO slots).
I'm not sure how to deal with this, and any help would be greatly appreciated.