I've got 6 varieties of Thyme going on. I've noticed my variegated Lemon Thyme has put out different looking branches since it started flowering. There are different colored flowers on one branch and un-variegated leaves on a few others. A couple of my Creeping Thyme's are also putting out some different colored flowers that are isolated to one branch. Is it possible that this is the result of cross pollination? I know that a lot of plants wouldn't show any visible signs of that until the seeds from the parent plants are grown, but can it go the other way around?
If your thymes are new this year, you've probably got some extras from the nurseries. I don't know if the variegated thyme will revert like other variegated plants might do.