> as a native (American) English speaker, his use of "doubt
> neither" in the context used, makes perfect sense to me.

Interesting. I, following my recollection from English lessons at school (focussing on British English but given by non-native speakers, mind you) would have used either of those exemplary expressions:

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

> I would think that both neither, or either would work the
> same and convey the same meaning (to an American anyway).

To me, "doubt neither of these" reads like the opposite, similar to "doubt none of these". I (wrongly?) understand "neither" as kind of contraction of "not" and "either".
Maybe a non-American native speaker can chime in and enlighten us about their use of either expression ;-) Thanks for your input, though.