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Problem cause:

There is an option in EP-Launch, I believe disabled by default, to allow more than 250 columns. In reality, it's actually 255 variables + one row header that gives 256 columns. So by default the CSV output generated by ReadVarsESO has maximum 256 columns.

This is due to the - now completely outdated - inner limitations of Excel. Indeed, before Excel 2007, you could only have 256 columns.

+-----------------+-----------+--------------+
|                 | Max. Rows | Max. Columns |
+-----------------+-----------+--------------+
| Excel 365*      | 1,048,576 | 16,384       |
| Excel 2013      | 1,048,576 | 16,384       |
| Excel 2010      | 1,048,576 | 16,384       |
| Excel 2007      | 1,048,576 | 16,384       |
| Excel 2003      | 65,536    | 256          |
| Excel 2002 (XP) | 65,536    | 256          |
| Excel 2000      | 65,536    | 256          |
| Excel 97        | 65,536    | 256          |
| Excel 95        | 16,384    | 256          |
| Excel 5         | 16,384    | 256          |
+-----------------+-----------+--------------+

(Source of table: superuser)

Solution:

In EP-Launch, Go the options, and find "Allow More Than 250 Columns" and check the box (I believe it sits under "Miscellaneous" according to the source code).

Side notes:

If you wanted to run ReadVarsESO directly without this limitation, you should read Calling ReadVarsESO without the 255 columns limit
The SQL file doesn't have such limitations and can always be queried for output variables.