I'd assumed Cygwin pipes are just Windows pipes, is that not the case?

Not a comprehensive list of problems, and not current but a good illustrative post of the kind of issues that people have run into in this post:

https://cygwin.com/pipermail/cygwin-patches/2016q1/008301.ht...

Its not that easy. Yeah, they are, but there is a lot of POSIX like glue inside so they work correctly with select() and other alarms. Code is very complicated.

But still, kudos for Cygwin Developers for creating Cygwin :) Great work, even tho it have some issues.