Most Helpful Girl
Relationship status changes no matter if they are going from Single to Relationship or Relationship to It's Complicated, or whatever, whenever there is a change, friends go nuts. "Are you okay?" "Oh when can I meet him?" "Who's the lucky guy?" And then you get stupid comments from friends you can't control like, "Aw damn there goes my chances" "Hope this one is better than the last one." Some people don't understand that their trite outbursts on FB can actually be really annoying and cause some hurt when they think FB is a forum to just show how cute and funny you can be when making a comment.
She probably took it down for this reason - to save the nosey people from commenting and just wants your relationship between the two of you. It's pretty obvious too that if you've been friends for a long time and now add you as the boyfriend that friends are going to make cracks she just doesn't want to hear about.
However, there IS a stigma attached that she doesn't seem proud to be with you. FB was originally made up to be a social business card with all of your stats in full view, and then later on as a way to celebrate what is going on in your life. If it really means something to you, tell her you want to scream it from mountain tops that you're together and ask her if she feels the same. I'm sure once she explains herself it will be clear. It's very likely just a privacy thing to spare the nonsense comments.1