Product Version = NetBeans IDE 7.2 (Build 201207171143)
Operating System = Linux version 3.0.0-29-generic-pae running on i386
Java; VM; Vendor = 1.6.0_24
Runtime = OpenJDK Client VM 20.0-b12

Note: Hints enabled

Sample code:
<?php
$b = $a; // Gives hint $a not initialised, which is correct
/*
 * some lines of stuff
 */
$c = $b; // gives hint $d unused, which is correct
?>

To demonstrate:
Load above code into editor. Hints are shown as indicated, in the left of the window and with markers in the right margin, as expected.
Position cursor over ~either~ occurrence of $b. 
The position marker for the other occurrence is not visible, being splatted by the hint marker.

Can be quite annoying when you think you've got all occurrences in a longer file covered, to find later there was another one (or more) hidden by hints!

Out of hint marker and position marker, which should have precedence? 
My vote is the position marker, as the hint can easily be found with the cursor at another position, but the hidden position cannot.