An inner join brings in columns that exist in both tables, not all columns from both tables. I am guessing that the join is the problem here. Depending on what exactly you're looking for, you will want an outer join of some kind.
I have the same problem with one file only containing more than 400 columns.
Only approximately 300 columns are imported in Tableau.
Does anyone know if there is a maximum number of columns allowed ?
The INNER join basically links the tables based on common columns, and bring all columns from both the table. The matching records will be retrieved and non-matching records will be excluded. So ideally there should not be any restrictions on number of columns from the tables, unless you specifically de-select them while adding the join. I doubt if this has something to do with the driver used for connecting the database.