I think there is a turning row missing. I think you work color #1 ending on a purl row, then purl one more row in color #1, then switch to color #2 begining with a purl row, and work color #2 in stockinette.
Edit - I mean to say that the random purl row is actually the turning row.
I did some swatches to show you what I am talking about:
Top as you described it earlier, purl with the new color one row then begin stockinette with the new color.
Bottom as I described above, purl with the old color then begin stockinette with the new color, starting with a purl row.
After turning to make the flap
Showing the turning row