I've heard a couple of people (out of many, many users) make this comment. It's not an issue with the Helio9's, and not something I have seen.
Some folks are very sensitive to PWM lighting, and can see flicker where others can't. The same folks are also often disturbed by the flicker of fluorescent lighting.
Make sure you have a good power supply. If the power levels are sagging, and/or or the supply is overtaxed, then the rise time of the voltage may be long enough make this more noticeable.
Also, as you stated, with different color settings, you don't see flicker. Setting the colors to a higher intensity will be better for folks who are more sensitive to the PWM.