Here's what I am able to reproduce. If a link is to a jpg - without the img tags - the lightbox of any other properly embedded images wrapped in links fail.
For example, code like this will execute a lightbox effect:
<a href="http://iblog.stjschool.org/demo/files/2007/04/salvador-dali-the-persistence-of-memory-15500.jpg"><img class="alignright" src="http://iblog.stjschool.org/demo/files/2007/04/salvador-dali-the-persistence-of-memory-15500.thumbnail.jpg" alt="" width="128" height="103" /></a>
but code like this anywhere else in the post will mess up the lightbox:
Notice the href ends in .jpg, but no image will be displayed.
In summary, avoid hyperlinks to images that are not embedded. "Link" to a page, but use "img" to embed images.
What I think is happening is that the lightbox-2 plugin uses java to search the post for images, it finds some, but then tries to use the tags it expects to find with each image(title, alt, height, width, src, etc), but doesn't find tags for the remaining images and the script fails.