I upgraded to the Mozilla 2.0 while using the Curacao theme and it did a odd thing to my bookmarks too. I could get to them with the mouse the first time I opened the browser- but then after that I could only get to them by using the CTRL/B combo.

But for me it was the theme that was the problem - I went back to look for new themes and there was an update/fix for the Curacao theme and now all is good again.