I had some problems, BUT :D after installing jQuery Colorbox 1.4 Release Candidate 3, most problems are gone because I can disable "Automate jQuery Colorbox" in options panel now. I don't want it everywhere on my site.
BUT!! how can I add class="colorbox-ID" to wordpress gallery's generated by the [Gallery] Shortcode?!
I have different galleries on different pages and I'm doing them directly in a template:
<?php echo do_shortcode('[gallery columns="4" link="file"]'); ?>