I noticed after sp1b, but I'm not using FSBUILT or other similar producs, and I've not updated airacs, so it is nothing linked to the navigation database/airports unless pmdg updated it with sp1b. However, if it works the second time, why it isn't on the first load?

Will have to try this approach some time later, as it has happened to me again and this time it was very annoying as I did not land well and really wanted to re-fly.Difference here is I am making my *.rte files via EFB and I am saving them with SID/STAR and RWY's. I will try saving them without and experiment more.Now backing in my memory I can't remember having such issue on first SP1.

Nothing at all - seems to be indeed something specific to SP1b.