DB2 Express-C on Mac OS X
To make it easier for future users to find a working answer:

It appears that one method to fix this problem is to create a symlink from the DB2 location to the Java Home you wish to use. Since I told DB2 to use my user when I installed it (this is for a development copy), the command I used to fix this problem was:

sudo ln -s /Library/Java/JavaVirtualMachines/1.6.0_29-b11-402.jdk/Contents/Home/ ~/sqllib/java/jdk64/jre