As far as I can tell, the two levels don't have any true difference other than price. If the planet has say, expert metal miners, there's an equal chance of finding it on either the first or second. Being that the chance of finding anything at all on a planet is on the lower end of the scale, the odds of finding *two* such goodies is even lower. This means that if you find nothing on the first go, it's very possible you singly got the short straw and missed the goodie. However, if you do find something on your first try, doing the second exploration is gambling on weather or not your planet has double bonuses.This means that if you find something the first time, the second upgrade will be statistically less effective.
Like someone else said, unless the second has a lower probability you are true, if not you are mistaken.
You are saying basically that once you roll a 1 on a dice, on the second roll you have a lower chance to get a 1 ...