Difference between "not every" and "every ... is not"

You are correct; Karan of the superuser question you referenced made a grammatical error. It should have been as you phrased it:

Not everything in DOS is plain-text

That being said, your understanding in the two examples you posted is slightly off. It should be

Every human is not a man. There is no human being who is a man.

Not every human is a man. There are human beings who are not men.

Such logic mistakes (especially with double negatives) are very common even among native English speakers. The fact that you are able to discern the intended meaning of Karan's comment, even with its incorrect phrasing, and your excellent grammar in this post tells me that you do not at all have a fundamental misunderstanding; on the contrary, your english seems quite good.

Your understanding appears basically correct. Also, the kinds of mistakes you have pointed out are indeed quite common.

Note, however, that the second part of the following item is not equivalent to the first part. (I've starred the second part to indicate its incorrectness as a translation of the first part.) The first part does not imply that humans exist; instead, it implies that if they do, then some of them are not men. The second part unconditionally asserts that human beings exist who are not men, a quite different statement.

Not every human is a man. *There are human beings who are not men.

Edit: The error of equating the two parts is an example of an existential fallacy, and if there were no humans, it would be an example of a vacuous truth. The wikipedia article about existential fallacies says

The existential fallacy, or existential instantiation, is a formal fallacy. In the existential fallacy, we presuppose that a class has members when we are not supposed to do so; that is, when we should not assume existential import.

One example would be: "Everyone in the room is pretty and smart". It does not imply that there is a pretty, smart person in the room, because it does not state that there is a person in the room.

...In modern logic, the presupposition that a class has members is seen as unacceptable.

The wikipedia article about vacuous truth discusses arguments for treating none, some, or all vacuous truths as “true”. (An argument related to non-equivalence of the example sentences is that the Implies operator and the Logical AND operator are not equivalent.)

I am sorry, there seems to be some confusion here. Your understanding of the following sentence seems slightly out of place:

Everything on DOS is not plain-text!

or as it stands corrected

Everything in DOS is not plain-text!

This does NOT mean that everything on DOS is not of the type "plain-text" (whatever that means). What this actually implies is that there might be some things in DOS that are of the type "plain-text" but not every one of them.

Generally, Everthing ... is not.. ... is inter-changable with Not everything is... However, there might be a few exceptions to that.