I found the problem, and the solution.
The problem is that Jar Bundler ignores any manual edits you make to the Classpath entries on the "Classpath and Files" tab.
The solution: once Jar Bundler has generated your app bundle, open the app folder and edit Contents->Info.plist. Find the ClassPath XML and manually edit it to look like this:
Save the Info.plist and re-launch your app. Should run just fine this time.
BTW, I also put junit.samples.AllTests as an argument to main rather than as a "parameter" property.