I ran into this issue today (same PKIX error) after setting up a brand new project and was completely confused since I had previously imported my security certificate for my organization using the steps outlined above. In fact, project performing a similar function did not have this issue.
I realized that the version of the MS SQL JDBC library Gradle was grabbing was the newest one (12.2.0.jre8 as of this answer) and my other project was using version 8.4.1.jre8. Once I specified the old version, I was up and running.
I realize this answer doesn't explain what about the new version is causing the issue but I'm hoping it helps someone in a pinch. I've wasted a lot of time on this already.
My project is using Spring Boot, Gradle wrapper, Java 8, JPA and MS SQL Server.