IIRC I had a problem like this and I solved it like this:
1) Click on the Tools tab and open up options.
2) The options should open up in a tab called Treeview, if not, click on that.
3) The 2nd checkbox down named Build Model BIF node in Tree should be checked in. If it is unchecked, click on it to check it in.
That should fix your problem, though I may be completely not remembering correctly how I fixed my problem, or this just doesn't apply to your problem. Hope I helped.