After waiting 5 minutes I take off and I'm told I don't have clearance to take off
Be sure you are on the hold short zone.
I never get to land from the east runways 24 25 etc. AI aircraft can But I'm always sent around to runway 6 or 7.
That's doesn't have anything to do with the scenery, that have all the runways in places, but it's a decision made by FSX using several factors (runway length, wind direction/speed, ils avail, etc.), each one with its own weight, with the wind having the most effect.
You'll always get the longest runway with an ILS, provided the tailwind component is not too strong to require a change of runway. That's how FSX always worked.