Why aren't dependencies factoring in auto-scheduler?

[ShaneNickersonNeustar]

I've built out a portfolio plan and linked all incoming/outgoing dependencies, given ticket estimates and resource capacity, but the auto-scheduler is still not factoring the dependencies. Anyone else have this issue or know what I might be missing? I'm having it only fill in empty values for target start/end date and still no luck. 

[Georgii Lumpov]

@ShaneNickersonNeustar an example would help. Without specifics It's hard to reply anything other that "well... it works for me" which is not going to be helpful in any way.

How does your plan look like? What are the estimates? Can you reproduce it in a smallest possible situation (like just 2 stories)? What's the expected result and what you see in reality?

Keep in mind there is a config parameter regarding treating dependent stories as well.