This can be caused by several factors. The most common cause is mic position. Experiment with different mic positions early and often to hone in on what works for your instrument. Audition with good quality, flat response headphones such as the ATH-M50. Then, after a few WaveMaps are created, test them out through your intended PA or acoustic amplifier. The best mic position for live sound is usually not the same as what you would want to hear on a studio recording.
Another cause can be the mic choice. If you have access to multiple mics, try them all. Flat, small diaphragm condensers (pencil mics) consistently give better results than large diaphragm or vocal mics. The flatter the response, the better. Move the mic farther away from the instrument. This often makes it sound more balanced and authentic. Try an omnidirectional mic – this can often make finicky instruments sound much better.
If you have an active system, make sure your battery is not depleted. Also, make sure your volume control is set about midway. Some systems run out of headroom when set to maximum volume, and that can interfere with training.
Make sure your pickup is not on the ‘pickups that don’t work’ list.