I had to adjust the plugin a little to make this work right in all browsers. I was using it in a little different way from you (function called directly from the template). If it doesn’t work, just restore a fresh copy.
Find the line in nggfunctions.php (line 44?) :
$swfobject->add_flashvars( 'file', NGGALLERY_URLPATH.'xml/imagerotator.php?gid=' . $galleryID );
change it to:
$swfobject->add_flashvars( 'file', NGGALLERY_URLPATH.'xml/imagerotator.php?gid=' . $galleryID . "&width=$width&height=$height");
