I'm always told to use runway 7L day or night, any kind of weather.
No, not in "any" kind of weather. FSX automatically selects a runway for takeoff or landing depending on MANY factors, the wind being one, but also the availability of an ILS (for landing), the length, the distance from the gate, etc. It's a formula where each parameter has its own weight.
You are being asked to always use the same runway, because FSX WILL always use the longest runway that has an ILS UNLESS the tailwind component is too high for that runway to be usable so, check your weather settings and, eventually, if you have a 3rd party weather program that controls weather.
The other thing is I'm ok to position and hold but never cleared to take off, As soon as I get airborne, tower tells me I'm not cleared for take off.
That might due to the issue of hold short zones being too far from the runway. Of course, we placed it in the correct place, but that doesn't mean the correct place is handed correctly by FSX. But if we placed it in the "wrong" place, in order to appease FSX, the logical position of the hold short zone won't match the visual position of the (custom) textures which are of course in the correct place, so people would immediately complain that the hold short is wrong, either because ATC won't clear them in the proper place, or because AI would hold short in the wrong position. And if we moved the visual hold short zones in the "wrong" place, to make the FSX ATC happy, people will rightly complain the scenery is not accurate to real world...