so do u have RewriteBase / in your .htaccess and is it uncommented?
if so, try comment it out (or remove) and see if it helps.
again, its hard to troubleshoot without the error logs, without knowing exactly what is it can not find.
Another possibility, is that your second domain is setup not to obey .htaccess, or not allow using mod_rewrite
so, at this point - who knows...