We just added this warning to our downloads page:
"Apple has recently (2008_09_24) released "Java for Mac OS X 10.5 Update 2". We highly recommend you do *not* install this! This Java update renders text boxes to be uneditable in the compiled version of CellProfiler. This occurs in both 10.4 and 10.5 (Tiger and Leopard)."
So if you have installed this update, it is apparently practically impossible to undo the Java update without re-installing the OS(!), according to Apple (I can't find the link right now). While this is not a great solution, we can provide you with the 1.5.0 Java frameworks that doesn't have this bug. It worked for one of our Macs here, but note, this may void your Apple warranty:
Download Java 1.5.0 from http://cellprofiler.org/linked_files/Java1p5.tar.gz
and untar it into /System/Library/Frameworks/JavaVM.framework/Versions/ with these commands:
tar xvfz Java1p5.tar.gz
Hopefully, Mathworks will get a fix for this soon. We have submitted a bug report with them, re: deployed applications.