This is very strange. Without seeing the code, very hard to guess why it's doing this.

But I do see it's in the early stage where Arduino is running "gcc -E" to discover which libraries are needed. Maybe it's an issue with the arduino builder program?

Any chance you could give the latest Arduino 1.8.3 are try? On Windows, you can download the ZIP file and extract is somewhere else on your PC, so it doesn't uninstall the copy you already have. Just remember where you put it, since you'll need to navigate to it when running the installer. Also pay attention to the title bar which shows the version, since you'll have 2 copies of Arduino on your PC and they look similar except the title bar.