Not really enough info to make an educated guess, but I recommend:
1. Make sure you're running latest OS 1.2.0
2. Unplug anything connected to MIDI In / MIDI Out or USB to Rev 2
3. Make sure you're connected to the main 1/4 outputs on rear
4. Power cycle Rev2 if its been on for a long time
5. Run Globals : Reset Globals
6. Run Globals : Calibration
7. Test with an INIT Patch (Hold the Transpose Down Button and Press Hold)
If its still not sounding right, contact support... they are very helpful and can offer up additional suggestions or support options.