I don't believe you have all your settings correctly setup for multistore to function as designed.
You have a mainstore.com, you can a a multistore only under these conditions:
1. subdomain.mainstore.com OR
2. someotherdomain.com
Note: you cannot have a multistore in just a sub-directory of you main store.
Next - in either one of the choices above of subdomain or otherdomain, you MUST point your document root to the location of your Main Store.
Once you have this done you will see on your main store - pages for products and categories the default store (main store) and other stores that you have created from the main store. You simply add a check to the box for each of the stores you wish that category or product to show up in. You control this from the master.
Please confirm that you have your stores setup in this manner.
Then when you go to the multi-store you can further control to show or not show any items that have been turned on for the multistore, and you can change the pricing for that multistore.
There is an additional line in the database for each product that is assigned to a multistore. but you do NOT have to recreate them, only turn the checkbox on.