I will try to explain this the best way I can

There are several ways to say it....
When someone is referring an application that they use within a specific operating system, the most common usages would be:
"I am running aMule on my Linux box"or
"I am running aMule on my Windows box"It wouldn't make sense to say
"I am running aMule under my Windows box" or
"I am running aMule in my Mac"... Those don't sound right at all hehe.
Now there is a difference between the statement that you run an application within a specific operating system and what you would offer as advice or offering instruction, or some other context.
Example 1:2nd person: "If you want to run aMule as a daemon, I would recommend running it under a Linux environment"another version: "If you want to run aMule as a daemon, I would recommend running it within a Linux environment"What you're looking at is essentially 2 different ways of saying the same thing
Example 2:"If you want to install aMule on Linux, you will want to check your distro repository for an official release.""If you want to install aMule in Linux, you will want to check your distro repository for an official release."Again, they both mean the same thing.
When it comes to software, on, in, and even under are somewhat interchangeable. Its a bit confusing, and trying to explain it is even more confusing lol. The reason is that software is not a tangible item, so on and in both work sort of the same way.
Performing an action (correct).... I need to put the luggage in the car.
Performing an action (incorrect).... I need to put the luggage on the car. (it will fly off!!!)
Performing an action (incorrect).... I need to put the luggage under the car. (you will run it over!)
Now with software....
Performing an action (correct)... I want to compile this application on linux
Performing an action (correct)... I want to compile this application in linux
Performing an action (correct)... I want to compile this application under linux
So in summation....
If your referring to a physical/tangible object, use the examples above. If you're referring to something nonphysical, then attempt to imagine a physical state and use the proper word accordingly.
Correct: I want to dive in the pool
Incorrect: I want to dive on the pool
There are exceptions though...
Correct: I run amule on debian
Incorrect: I run amule in debian
Thats about all Ican think of. Hope this helps!