UPDATE: You propably will not be able to run java -version as stated before...
A closer look to your echo $PATH output shows the part:
In a previous posting, I saw a path like
If running java, bash looks all directories in $PATH from first one to the last one. The first occurence of en executable "java" program will be launched.
With your current $PATH, you will start something in /usr/lib/java/bin, if present, or in /usr/lib/jre1.6.0_01. But nothing in /usr/lib/jre1.6.0_01-bo6/bin, what I suppose you to want.
Sound weird. ;-)
You can clean your classpath, or (the dirty way), you can export the $PATH with
This way, the first directory, bash looks for your java, is /path/to/your/jdk/bin. All remaining directories will be ignored.
Less work, but little dirty.