Does the theme editor always work??

Question... I was making a color graduated vertical meter, and it was different over the variety of tracks.  Some tracks it was as intended.  Then other tracks the colors were just alternating bands of color, unlike how it was created in the theme.
I haven't run into this with other items, except some "patches" of area would seem to be affected.  Later on after opening Sonar again, it might be gone or still there.
IOW, seems some fluky-ness is going on.