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Every now and then when I modify only one of the classes, save and package the whole project with jar, the size nearly doubles and class loader gives "bad header" errors. If I do a "Rebuild All", and jar them the same way, things go fine.
How do you perform the packaging ?
jar cf jarfile.jar com\mycomp\myproj\*.class
How many times has it happened? Are there any similar steps or types of source changes? Is it always the same source file? Do you still have one of the bad jars? The next time it happens, can you examine the output directory for the project to see if anything appears different before/after the next full build.
Closing until we get more information. Please reopen when you have more details.