Robert, Illuminated Cloud generates a package.xml when deploying through the metadata API. Let's gather some additional info on exactly what it's trying to deploy. Go into
Help>Debug Log Settings and add the following entries:
#com.illuminatedcloud.intellij.builder.ForceComBuilder
#com.illuminatedcloud.intellij.builder.ForceComMetadataApiDeployer
Rerun the force save and send me the resulting info in idea.log (Help>Show Log in Explorer/Finder). Feel free to send it via email if it contains sensitive info.
Regards,
Scott