The code loops over directories, retrieving users from each, but exits the loop when it has the number of users that should be returned, despite the fact that it started from zero, not from the startIndex.

so at line 648:

if (!isAllResults && (results.size() >= query.getMaxResults()))

query.getMaxResults() should be totalResults

edit Actually, even that fix contradicts this comment above the loop:

        // we require every directory to return <code>totalResults</code> results instead of
        // <code>totalResults - results.size()</code> because the users returned could be duplicates of existing results

So the break should be removed.