I ran into an issue today. I have a site Content Type that defines several list fields and I have a specific order for those fields to be displayed. Today I added a new site column to this content type and I updated the order of my fields in the content type as usual. However, the lists that use this content type became all out of whack in regards to the order of the fields. I tried to update the order in the Content Type again and push down the changes, but never had any luck.
So, being a developer, I wrote up a simple console app that will iterate through my sites (about 40 webs) and find my particular list and content type and reset the order of the fields to match the parent content type.