very strange, indeed;

it is likely you found a bug, and, with mentioned 5.8.0, it is not very strange: current 5.8.8 version has many bug fixes.

It is very likely an internal bug hidden inside cygwin perl internals, I bet it is caused by \r\n->\n struggle.

I suggest you to try newer perl version on cygwin, and, if your problem persist, narrow down a problem and file a bug report.