zipdiff works perfectly when the two zip files have the exact same path tree. If you compare different version of software distributions, however, it is very likely that the root folder contains the version name or date.
The attached patch adds the options --skipprefixes1 and --skipprefixes2 which allows the user to sets the number of leading directories to ignore. This works similar to -p on the unix patch command.
This patch is fully compatible with command line tools, ant skripts and classes using jardiff. Only classes that extend DifferenceCalculator might need to be adjusted.