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it would be helpful to know a little bit more about the several instances you've referenced: Database edition and version, APEX version, APEX Listener version (also the one you've exported from), JEE Container used to host APEX Listener, charset of the file you're trying to import.
I don't have this issue when using valid application archives with the appropriate charset. However, if you import with a charset different then your export, e.g. you have a UTF-8 file and import it with some ISO charset or vice versa, strange things can happen...