>> "I doubt neither of these changes weren't made in the main exe [...]." ;-)

> The last sentence above does not sound or read right to me.

It is formally correct in terms of content, i.e. a true proposition, just not easy to decipher due to the combination of 3 negations. Indeed, nobody in his/her right mind would say something like this in a normal conversation, though. It's better suited to exercises in propositional logic, hence the smiley.

> I think you are getting mislead by focusing on the combination of
> "doubt neither", instead of separating it into "doubt", and "neither
> of these changes", but I might be wrong in what you are thinking.

Yes, I think you are wrong here. I'll try another way of explaining exactly how I process the meaning of the expression "I doubt neither of these changes were made in the main exe [...]." I start with the basal (but obviously false) proposition in (1) and progress from there by adding the preposed constituents in (2) and (3):

(1) "these changes were made in the main exe" = A
(2) "neither of [A]" = not A
(3) "doubt [not A]" = not [not A] = A

As can be seen, the outcome of (3) and thus overall meaning of the expression equals the meaning of the false proposition in (1). Of course, this is unless the concept of two negations intensifying the negation instead of cancelling one another is applied.

> Better to just accept what Jacek wrote about double negatives
> being used often in English.

It wasn't Jacek, and I know about this concept (after all, there are German dialects using this concept in certain contexts as well, like Bavarian). Just to get you right, do you as a native English speaker read the sentence in question as a case of negation-intensifying double negation?