The fact that your EPUB eBooks are (properly?) displayed by some reading systems does not make them valid with respect to the EPUB specification and you should seriously consider fixing them.
Said that, the only real alternative to epubcheck is, for EPUB 2 files only (i.e., not for EPUB 3 files), flightcrew, which is the validator embedded in Sigil but it is also available with a CLI:
http://code.google.com/p/flightcrew/