Actual rendering is done by Giancarlo's Nebula Renderer. NRGUI is just passing rendering configuration (parameters) to Nebula Renderer.I remember there was a glitch (distortion) problem with one of the older renderer versions. It was fixed then Giancarlo - since then no problems were reported.
I guess you are using the latest NRGUI and Nebula Renderer. If not, please do upgrade to the latest version. Otherwise, you should contact Giancarlo (I am currently on a vacation and send him a short piece of problematic audiofile (original and processed versions). You should also send him the rendering procedure - file NR.BAT located in NRGUI folder (this is the actual procedure which is executed when rendering). If you've saved config to NRGUI template, then this one would be also fine to attach.