I don't see how that fixes the problem at hand. Could you please elaborate on the specifics of how you see this working?
I don't know if you have seen it but I am the maintainer of the Drupal Shadowbox module.
http://drupal.org/project/shadowboxThe module provides an admin interface for Shadowbox to set all the options and also for what media types to support.
Using the custom build as you suggested doesn't fix this issue for us. Sure, there is an option to not include Sizzle in the package but that problem is already fixed. Users still want to display Flash media on their sites but would mostly be using Drupal's swftools module, rather than anything built into Shadowbox.
The problem is that the Shadowbox code needs fixing because we have found a case where it is not robust enough to cope with our needs. Can you have a proper look into this issue please?
Just to give you an idea of how many people this affects:
http://drupal.org/project/usage/shadowboxThis is just sites so imagine all the users of those sites seeing these error messages!