Cucumber in Intellij failing to use certificates - intellij-idea

Question

When running a Cucumber test, using cucumber.api.cli.Main, the test is failing to recognise the certificates that are installed in the JDK.
I am running using the following:
IntelliJ 2016.1.2 (Build #IU-145.972)
JRE 1.8.0_74-b02
Plugin Cucumber for Java version: 999.999
It works, when run from the following gradle task, from the command line:
task functional(dependsOn: ['testClasses']) << {
javaexec {
main = "cucumber.api.cli.Main"
classpath = sourceSets.test.runtimeClasspath
args = ['--tags', '~#wip',
'--plugin', 'junit:build/junit-test-report.xml',
'--plugin', 'pretty',
'--plugin', 'html:build/cucumber-html-report',
'--plugin', 'json:build/cucumber-json-report.json',
'--glue', 'step_definitions',
'--strict',
'src/test/resources'
]
if(project.hasProperty("coverage")) {
jvmArgs = ["-javaagent:${configurations.codeCoverage.asPath}=destfile=${buildDir}/jacoco/jacoco.exec,sessionid=HSServ,append=false"]
}
}
}
But when I create a Run Configuration for Cucumber, using:
Main Class: cucumber.api.cli.Main
Glue: step_definitions
Feature or Folder path: /Users/xetius/application/src/test/resources/system_tasks/request/validation_handling/request/validate_hardware_fulfilment_request.feature
Program Arguments: --plugin org.jetbrains.plugins.cucumber.java.run.CucumberJvmSMFormatter --monochrome --name "^Pending details$"
Working Directory: /Users/xetius/application
It fails to recognise the certificates for connecting to the remote services.
I have configured IntelliJ to boot using the external JDK, into which I have installed the certificates using keytool, and I can see that it is using this JDK when running the configuration. I have also tried configuring Server Certificates, and importing the same certificate.
However, within IntelliJ, it throws an exception when connecting to remote services. It is also throwing the exception when gradle is run from within the IntelliJ terminal.