I'm confused, if you're navigating away from one table to another, why would you expect filemaker to make any assumptions for you based on the first table? Tables are related yes, but their sort orders, found sets and focused records are all independent. FileMaker does remember those things though, because if you navigate back to the first table using "go to layout", you'll be in the same found set, sort order and position that you were in when you initially left.
Native behavior, if you're using the "go to related record" script step, is to put focus on the first related record through the relationship. Still, your second table really has nothing to do with what's focused in the first table.
Of course scripting your navigation is ultimately the easiest way to have complete control, maybe I'm just not understanding what your issue is, but it sounds like you just need to understand the default behavior.