Oh, and by the way Shane, if you were able to make c:\jdk1.3.1\bin\javac.exe work, then c:\jdk1.3.1\bin\
javadoc.exe should also work. Just javadoc all your code from the command line if need be. I usually write a batch file for each of my projects to do my javadocs.
Let me recap the current state of affairs here so we are on the same page:
1)You can compile from your JCreator
2)You can compile from the command line using c:\jdk1.3.1\bin\javac.exe
3)You can't compile from the command line just using javac.
If these are the correct facts, you are OK.
You should be able to do everything you need to do.