Have you tried this?
I'm guessing this is a somewhat fresh install.
1) Install a second copy of WordPress, using a second table_prefix.
2) Using something like PhpMyAdmin, drop all of the tables with the new table_prefix EXCEPT "options".
3) Open up the config file, and change the table_prefix to the original table prefix.
4) Open up wp-settings.php and scroll down to about line 75 or so, where it lists the table names. there will be a bunch of lines like:
wpdb->tablename = table_prefix 'tablename'
edit the line for the options table like so:
$table_prefix . 'options'
Note: new_prefix is the prefix you used in the second install, which is different from the first. So, if your new prefix was blog2_, the edited version would look like:
This way, you're using the options/settings from the second install, and can customize it separately from the first.