@dkayiwa - I was able to fix the issue, it turned out to be a permissions problem after all.
I had downloaded the ref app distro omod files from sourceforge as a zip file and used the sudo command to unzip them into the OpenMRS server’s modules folder. Because I had used sudo, the ownership of the omod files was root and not tomcat7. Running chown and assigning the ownership to tomcat7 solved the error.