The DocumentMarkers code in Document.cpp assumes that everything is painted into the root. It needs to be educated about compositing layers.
Created attachment 43633 [details] Testcase with 2D transform
Created attachment 43726 [details] Patch
Comment on attachment 43726 [details] Patch r=me (made some comments in person, and Iām told there will be a test :) )
http://trac.webkit.org/changeset/51324