FYI, we have our Tomcat installations located on E:\Tomcat. We've never been able to get patching using Shavlick to work properly for the last three patches released for Tomcat 6. The patch seems to install the update, but it ignores our custom install folder and just installs into the default path that the Tomcat installer uses when first fired up for an install.
Just FYI.
To duplicate, install Tomcat 6.x in a custom folder, then patch it, you will see it ignore your pathing.