I've looked into cause of failure for 
css3/selectors3/xml/css3-modsel-61.xml

What happens is that a background specified by:
div.stub *:not(:link) { background-color : lime }

does not get painted. The bug is timing dependent, sometimes it happens, sometimes not. CSS is in external stylesheet, that is what causes the flakiness.

The fragment trees generated when bug happens, and when rendering is correct differ:

FAIL:
.:: LayoutNG Physical Fragment Tree ::.
  Box (block-flow children-inline) offset:unplaced size:800x18   LayoutNGBlockFlow div class='stub'
    LineBox offset:0,0 size:287x18  
      Text offset:0,0 size:287x17  start: 0 end: 42

SUCCESS

.:: LayoutNG Physical Fragment Tree ::.
  Box (block-flow children-inline) LayoutNGBlockFlow div class='stub'
    LineBox offset:0,0 size:287x18  
      Box (inline children-inline)  LayoutInline a
        Text offset:0,0 size:287x17   start: 0 end: 42


I think what happens is that when the stylesheet loads, there is only paint invalidation. Because in NG, BoxFragment is optimized out
if there is no background, for NG we would either need 
- layout invalidation when backround color changes for inlines
- stop optimizing fragments away if there is no background.