It is very good, that the Eclipse team changed the color of marked
occurrences from yellow to gray, since yellow was too similar to warnings.
But unfortunately they only (or mostly) seem to test eclipse on Windows.
On Linux this gray is too similar to the standard gray of SWT background
and is therefore almost undistinguishable from the background (right to
the scrollbar).
Could you maybe change the color to something useful and maybe add a
configuration entry for this color?