Does this disparity survive blocking? Your gauge will naturally loosen up in a large piece anyway, possibly by half a stitch or more. (I did not know this, until I came across this entry on the Yarns, Etc. blog
. It's about halfway through the article when Erin begins talking about gauge on the Katie Pullover she was about to start.)
That said, that phenomenon usually affects the gauge of the entire
piece, not just the CO/BO sections. So maybe that's not it either. But it's worth checking the actual gauge at both ends pre- and post-block to see.