We found that the CTRE tutorial was outdated and it was best to use the example projects on Github as models (
https://github.com/CrossTheRoadElec/FRC-Examples).
Following these instructions seemed to solve our build problem:
1: Download CTRE Toolsuite (No Installer) package 4.4.1.9 (.zip) from
http://www.ctr-electronics.com/hro.h...ical_resources
2: Extract the downloaded Zip file.
3: Take the Java folder and Copy and Paste the entire folder into wpilib/user/
4: If you have any questions refer to the README in the root directory of the zipped folder.