this has nothing to do with subgroups. When I create a new contact from a phone number, I'm not indicating any group. The new contact will be found by the phone wide search, but not within the phone app, or the contact app.
I sync via MobileMe, and all my contacts and edits sync as they should, except for those new ones created from within email, phone, or contacts.
This is clearly a bug, and it's maddening that since this thread started in August, nothing has been done about it by apple.
iphone 3G, OS 3.1.2