PowerPivot removed table replicated into the data model on refresh

Hey
I am facing the following problem which is absolutely persistent and annoying in nature. I am using a data model created with PowerPivot with connections to three different SQL servers and 25 tables. The bug is that every time I refresh my data, a table
that was initially added to the data model (and later removed) is replicated in equivalent number of tables that use this connection, which is currently around 12 tables, so I get 12 duplicates of the same unnecessary table on every refresh, named with the
name of the schema on the SQL server that is followed by a running number. Removing these from the data model on every refresh simply takes too much time on a daily basis. The additional undesired table which is created is what is defined in the SQL query
of the connection string of this connection.
I tried to solve this problem by zipping the Excel file and modifying this SQL statement present in the connection string in the connections.xml file in a way that it would not return anything, but this always leads into a corrupted workbook.
After encountering this I have managed to avoid this problem by making sure that the initial table I'm adding to the data model will remain in the model, but I really don't want to rebuild this current model. Is there any fix for this issue without
rebuilding the data model?
Thanks for all the help in advance!

I am using 64-bit Office 2013 with the recent SP1 upgrade and the included PowerPivot plug-in on a Windows 8.1 machine.
I always create the connection by using "From SQL server" then fill in the server and log in details and use a ready SQL statement that I have written by using SQL Server Management Studio to import the initial table. For all the preceding tables
using the same server and schema, I always select it from existing connections and just paste the SQL queries required for any additional tables to the "Write a query that will specify the data to import", rather than using the table import tool.
I am not sure if it could have any effect that I've been using the type connection "From SQL server" although the database is really running on Azure (there is a possibility to select From Other sources > Microsoft SQL Azure, but the functionality
seems the same).
I don't really understand what I should edit from the existing connections section. Just to clarify, apparently the Connection String parameters can be edited from PowerPivot, but not the Command Text which can be viewed from Excel Data > Connections
> Properties, but is shown in gray with a message "Some properties cannot be changed because this connection was modified using the PowerPivot add-in."
In the data model I am using two sets of identical tables, but connected to two different servers that are running a database 1:1 in structure. Initially the problem considered only the other of these, but I accidentally reproduced it by, again, editing
the SQL query in the table that was initially imported when that connection was created (PowerPivot > Design > Table Properties). Now when refreshing I get tables that are structured as in what the "Connection Text" part of the connection would
produce, which replicated for the equivalent amount of additional tables using the same connection, so now I'm getting 12 tables (the number of tables using the same connection) each named "*schemaname1* Query", "*schemaname1* Query2",
"*schemaname1* Query3" "*schemaname2* Query" and so on.
Personally I can definitely see a pattern here. If there isn't a table matching what has been specified in the "Command Text" that was described when the connection was created, then it for some reason runs this query anyway on every table that
is using the connection.

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