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FYI, a "stack overflow error" could come on a 32 bit machine (or even a 64 bit machine) since the java stack size limit is settable on the java command line. Also very poor code in the epub could result in a near-infinite loop in some recursive search routine quite easily, and that would eat up almost any size java stack.
If you run a simple Sigil Well-Formed check on the epub before running the epubcheck plugin does it report any problems?
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