Issue only seems to affect Chrome on Linux. Firefox and Midori render correctly. Screenshot is from Chrome 28 on Fedora 18. Flat UI 1.1
That's because of fonts difference — not enough space for all components to fit into one horizontal row. Try to shrink horisontal paddings of the search form for example and it will fix this bug.
Fixed in 1.2 and here is a diff if you don't want to wait on official release:
@@ -417,7 +417,7 @@
border-left: 2px solid mix(@base, black, 85%);
border-bottom: 2px solid mix(@base, black, 85%);
- padding: 8px @navbar-link-space 6px;
+ padding: 8px 0 6px @navbar-link-space;