Since it seems that you are more active on this forum, I'm cross-posting this.
I upgraded from MF 1.X and WP 2.9 to MF 2.x and WP 3.0 and what I noticed that not all of my fields where showing now.
Then I started to add missing fields and noticed that if there was field with that title (but different custom field key), that field would be deleted so only newly added field was showing.
Did you make this intentionally or it is a bug? In old versions everything worked great and I had even several fields with same title but different custom field keys. Although it maybe looks odd to have several fields with same title, there is a usage case.
I would appreciate if you would give me answer so that I can plan further steps since this was on production site.