Version:           KDE 3.90.1 (using KDE Devel)
Installed from:    Compiled sources
Compiler:          g++ 4.1.1-51.fc6 
OS:                Linux

The KatePart doesn't highlight with the proper formats if the syntax scheme specifies the same defStyle with different modifiers applied. An included style which suffers from this problem is the Scheme one: if you enter something like:
(((((((())))))))
in KDE 3.5.6 KWrite and set the highlighting to Scripts/Scheme, all the parentheses are of a different color. If you enter the same in KDE 3.90.1 KWrite and set the highlighting to Scripts/Scheme there too, you get everything in purple instead. The "offending" code in scheme.xml is this:
      <itemData name="Brackets1"    defStyleNum="dsNormal" color="#ff0000" selColor="#000000" bold="1" italic="0"/>
      <itemData name="Brackets2"    defStyleNum="dsNormal" color="#ff8800" selColor="#000000" bold="1" italic="0"/>
      <itemData name="Brackets3"    defStyleNum="dsNormal" color="#888800" selColor="#000000" bold="1" italic="0"/>
      <itemData name="Brackets4"    defStyleNum="dsNormal" color="#008800" selColor="#000000" bold="1" italic="0"/>
      <itemData name="Brackets5"    defStyleNum="dsNormal" color="#000088" selColor="#000000" bold="1" italic="0"/>
      <itemData name="Brackets6"    defStyleNum="dsNormal" color="#880088" selColor="#000000" bold="1" italic="0"/>
I also have some highlighting descriptions of my own which use this feature and thus don't work either. The common point is that they all use differently-modified versions of "dsNormal".

NOTE: I already noticed this bug in KDE 3.80.3, but I figured you're probably working on this already. However, unfortunately, it is still not fixed in 3.90.1.