Thank you for your help in diagnosing this.
For more detail on why the blog ids are assigned in this way see my reply to your other thread. Normally the blog_id should not matter in network_active installations, except for the following:
There is a bug in the code that displays balances in the admin backend. Addresses and transactions are filtered by blog_id even in network_active installations where they shouldn’t be.
Note that there is no issue with the actual balance calculations as they are used to process transactions. Only with the display in the admin screens.
This will be fixed in wallets version 5.0.13. I will notify you here about this.