We've had security software in the past break software compilation in this method by replacing entire files with zeros. I'm not saying this is the case, but it wouldn't surprise me if it were.

Basically the linker couldn't open the file on windows (because it was locked by another process scanning it), and didn't error. Just replaced the object code to be linked with zeros.

People couldn't figure out what was wrong until they opened a debugger and saw large chunks of object code replaced with zeros.