When using the MVC pattern if you use a stores array config in the controller the framework will automatically create a convenience instance of the store with the ID being the last part of the store's class name (i.e. App.store.MyStore will automatically create a store instance with storeId of MyStore).
What you can do to circumvent the shared store issue is set an alias on the definition of the store like:
Then when you instantiate the grid on your two panels you'll config the store like:
Now your grids will have the same store type, but not the same store instance.
// any other component specific store configs if any