Only on my Mac Mini this is happening (OS X Yosemite 10.10.2) and it just started yesterday. Whenever I start Chrome it shows all my bookmarks and when I click one of them (doesn't matter which one) they all disappear including the bookmark bar area. If I close Chrome and restart it they appear again, but the problem repeats itself.
Best Answer
Press ⇧⌘B to always show the bookmarks bar.
That's not the bookmarks bar—that's just bookmarks from your bookmarks bar being shown on the New Tab page.