You were charged the full fare because you travelled on 11 October, but your Dal Voordeel season ticket is valid from 12 October. As of today, you will be charged the reduced fare if you check in during off-peak hours.

Also note that since you have an NS Flex subscription, you will now travel on invoice, not on balance any more. You will get an invoice at the end of each month for the travel costs incurred and the season ticket costs of the next month, which will be withdrawn from your bank account automatically. The remaining balance on the card will no longer be used. You can have it paid out to you at a service desk.

Addition:

Just to be sure, before your next travel, go to the ticket machine and check if the season ticket product markers are properly loaded on your OV-chipkaart.

When in doubt, use "pickup order" ("ophalen bestelling") to synchronize your OV-chipkaart with the central computers.

Also, you do not need to and you cannot buy 40% discounted train tickets for yourself, only for fellow travellers (check conditions first).

You pay for your own travels by checking in and out your OV-chipkaart.

Remaining card balance should be automatically invoiced and payed back to your bank account by NS, unless you have an old style "Dal Voordeel op saldo" (unlikely).

Since Romanser states the card was ordered on 5 October and the starting date of NS Flex is 12 October, I think it's safe to assume a new card was ordered together with the NS Flex season ticket since a week after ordering NS Flex with a new card is the first possible start date. This means NS Flex was already loaded onto the card when it arrived and no action at a ticket machine is required. It also means the balance will not be reimbursed automatically, since it was loaded onto the card after NS Flex was.

You can get the remaining balance (€ 22,80) back at a service desk (e.g. Leiden or Amsterdam Centraal), or maybe https://www.ov-chipkaart.nl/en/credit-refund will work without having to send the card to OV-chipkaart.