If both stores are using the same database, you should be getting the same results.
Zen Cart doesn't care what folder your store is in, as long as you properly specify its location in your configure.php files.
The only exception to this is if you're storing session data in files, you'll need to update your Admin->Configuration->Sessions->Session Directory setting to point to the correct new path. The classic symptom of this being incorrectly set is that items no longer get added to the cart and logins don't work, after moving to another folder/server.

As for your date issues, it sounds like you've got some logic wrong somewhere in your custom code.