Ok, I have thought about this some more and I think I know what the problem is.
When you are knitting the mitten, you place several stitches on a holder. The side of the stitches that points toward the top of the mitten is the knit side of the knitting.
However, when you go back and knit the thumb, the stitches on the stitch holder become the bottom part of the thumb (you pick up a couple of stitches for the very top of the thumb). So, you end up knitting around on the side of the stitches that points toward the thumb.
does that make any sense? So it sounds to me like this is a pattern issue, and if I use this pattern again (which I am right now, I’m making another mitten and hoping it will come out better LOL) I should just purl the thumb all the way.
Does that make sense to anyone? If so I will go to the thread that Ingrid linked to and explain to that poster what the problem is for future ref as well.