Intelligent Reports needs to communicate over https with JIRA. If your instance of JIRA is using an invalid or self signed certificate to run https you will need to install that certificate as a trusted certificate.
To install the trusted certificate you need to install it into the trust store that JIRA is using. If you have the JAVA_HOME variable set correctly you should be able to use the following command:
$JAVA_HOME/bin/keytool -import -file certificate.cer -alias tomcat -keystore "$JAVA_HOME/lib/security/cacerts"
%JAVA_HOME%\bin\keytool -import -file certificate.cer -alias tomcat -keystore "%JAVA_HOME%\lib\security\cacerts"