I upgraded a couple of my machines to 10.3.9, but not our main production machine. Reading of various problems over the weekend gave me pause, and apparently with good reason.....
Java and Safari issues after updating to Mac OS X v10.3.9:
After updating to Mac OS X 10.3.9, some systems may have issues with Java applications and Java-enabled websites when using Safari. Safari may unexpectedly quit, and standalone Java applications may unexpectedly quit or not launch.
You can perform a simple test to verify whether your computer is experiencing this issue. If it is, you will need to reinstall one or two software updates to resolve the issue.
Verifying the issue
Go to the Utilities folder inside your Applications folder.
Open Terminal.
Type:java -version
Press Return.
If this issue affects your computer, you will get the the message, “Segmentation fault” (if you don't see this, your computer is not affected by this issue). To resolve the issue, reinstall one or both of the following software updates.
