TL;DR: All the problems I had with the money transfer is now solved!
So, I’ve given my employers details to directly transfer money into my account. The money is deposited without needing me to fill up a form. So, I guess they were being all formal when it was sent to their intermediary account.
Our best guess at this point is that the intermediary bank were missing out on details all the time. And then my bank would have to ask them for more details and then they would send an addendum with the clarification. Meh. Problems solved. Twice I’ve recieved direct transfers to my account and both times I got at the end of the second working day!