superprg. Your categories are gone because you need to reset the categories each time you create a store. Go to the admin, select the template for each store, and set the tools->layout boxes controllers for each store.
Actually because this, and the other setup requirements for each store I've created an additional admin tool to quickly generate each of my subdomain (multisite module) stores. One of the steps it takes is to populate the "layout_boxes" table with all the boxes I want enabled. Using the template below I just do a find-replace on $$STORE_NAME%% with your store name then import it: "mysql -u root -p <database> < layout_boxes.sql"
Of course this only makes sense if your going to be creating quite a few stores with your MultiSite install. I have around 30, and it works very well.
Here's the sql I use. I would suggest getting one of your stores boxes exactly the way you want them and dump out layout_boxes so you can do this with your own settings:
INSERT INTO layout_boxes VALUES
(NULL,'%%STORE_NAME%%','banner_box.php',0,0,300,1,1),
(NULL,'%%STORE_NAME%%','banner_box2.php',0,1,15,1,1),
(NULL,'%%STORE_NAME%%','banner_box_all.php',0,1,5,0,0),
(NULL,'%%STORE_NAME%%','best_sellers.php',0,1,30,70,1),
(NULL,'%%STORE_NAME%%','categories.php',1,0,10,10,1),
(NULL,'%%STORE_NAME%%','currencies.php',0,1,80,60,0),
(NULL,'%%STORE_NAME%%','document_categories.php',0,0,0,0,0),
(NULL,'%%STORE_NAME%%','ezpages.php',0,1,-1,2,1),
(NULL,'%%STORE_NAME%%','featured.php',0,0,45,0,0),
(NULL,'%%STORE_NAME%%','information.php',0,0,50,40,1),
(NULL,'%%STORE_NAME%%','information_footer.php',0,0,0,0,0),
(NULL,'%%STORE_NAME%%','languages.php',0,1,70,50,0),
(NULL,'%%STORE_NAME%%','manufacturers.php',0,0,30,20,1),
(NULL,'%%STORE_NAME%%','manufacturer_info.php',0,1,35,95,0),
(NULL,'%%STORE_NAME%%','more_information.php',0,0,200,200,1),
(NULL,'%%STORE_NAME%%','music_genres.php',0,1,0,0,0),
(NULL,'%%STORE_NAME%%','order_history.php',0,1,0,0,0),
(NULL,'%%STORE_NAME%%','part_finder.php',1,0,0,0,0),
(NULL,'%%STORE_NAME%%','product_notifications.php',0,1,55,85,0),
(NULL,'%%STORE_NAME%%','record_companies.php',0,1,0,0,0),
(NULL,'%%STORE_NAME%%','reviews.php',0,0,40,0,0),
(NULL,'%%STORE_NAME%%','search.php',0,1,10,0,0),
(NULL,'%%STORE_NAME%%','search_header.php',0,0,0,0,0),
(NULL,'%%STORE_NAME%%','shopping_cart.php',0,1,20,30,1),
(NULL,'%%STORE_NAME%%','site_links.php',0,0,0,0,0),
(NULL,'%%STORE_NAME%%','specials.php',0,1,45,0,0),
(NULL,'%%STORE_NAME%%','tell_a_friend.php',0,1,65,0,0),
(NULL,'%%STORE_NAME%%','whats_new.php',0,0,20,0,0),
(NULL,'%%STORE_NAME%%','whos_online.php',0,1,200,200,0)
Hope this helps.