First try the most recent update of 1.4.2, which is 1.4.2_15 at http://java.sun.com/j2se/1.4.2/download.html.
If the problem still persists, try to include more details about what you think is slowing down. What response time are you talking about -- the keyboard, GUI elements on the screen, or ...?
It may be worth checking garbage collection time. Add options to the java command line to trace garbage collection behavior:
in 1.3.1, add:-verbose:gc
1.4.2_xx, add: -verbose:gc -XX:+PrintGCDetails
and save the output to a file. See if the times are approximately equal.
Also post your java command line, and the type of hardware you're running on, including the amount of memory on the machine.