Swedish trains are best booked on the SJ website. You need to add the Interrail discount in the "Who will travel” section. It asks for a pass cover number but isn't very picky and will happily accept any number that consists of a capital i and 8 digits (it isn't printed on the reservation).

The rail planner app is only updated once a month so for making detailed plans the advice is to use the planner of the German railway (DB) or the planner of the national railway where you will travel.

It is best to make the reservation at the national railway, in this case 

https://www.sj.se/en/home.html#/

In order to make a reservation at sj.se you need a Pass Cover Number that you have to request from Customer Support. You can use this form to contact Customer Support. Please let Customer Support know when you are planning to start travelling and let them know that you need the Pass Cover Number now.

https://eurail.zendesk.com/hc/en-001/requests/new

I just looked at the train you want to book and took the advice of @rvdborgt to enter I12345678 as Pass Cover Number and it worked fine. If you want a seat on the train, you select the 35 SEK option. If you want a couchette, you start by selecting the 230 SEK option. You will then get more options on the next page.

Thank you tons, @AnnaB and @rvdborgt! This was very helpful and now I can get excited again after a minor frustration  

Did you manage to book the 23:09 train? Thats the one i’m trying to book too, and can’t find it on the SJ.se website either?

This overnite does NOT run nites sat/sun. Maybe thats why? It will certainly show up in sj.se

Why would it be on the rail planner then ? It’s the Friday night too not saturday ? 

@Tiiuli @adamwilson06 

There are construction works on the rails so there is no train leaving Stockholm for Malmö just after 23 on the 10th of June.

There is a high speed train leaving Stockholm at 19.21 and a night train leaving at 21.04.