Did you check the permissions of the accounts thta you are using to connect to the SQL table? Also did you check to make sure that they werent views? There are some options when you establish the External Source that you can play with.
Double check your System DSN and make sure that it is not set to connect to that sub-folder.
As Mr Vodka mentioned, you should check with your database administrator (DBA) to make sure your SQL account has privileges for listing the tables in the database.
Second, you should just use the default settings for the "Filter by Type" checkboxes when configuring your External Data Source (in other words, only the "Tables" checkbox should be selected).
It is possible that the tables you want to see aren't really true tables - instead, they are "Views". If that's the case, you should also select the "Views" checkbox.
With either of these settings, you should indeed see only the tables (and views), with no system tables. If you don't see your tables, then there is very likely a permissions issue with your SQL account. Your DBA should be able to fix that.