I haven't used Womble in a while, but when I used to strip the pulldown there were occasionally time code errors in the file that DGPulldown generated, so I used to run the GOP fixer twice: once after demuxing and once after DGPulldown had stripped the pulldown. It's time consuming, but usually it worked.
Of course, removing the pulldown used to create problems with videos with non-film material. That's one reason I don't really use Womble any more.