Thanks to Ian above for providing me with a pointer as to what the additional configuration was.
To resolve this I had a look at ivysettings.xml in the jar. In ivysettings-local.xml i saw what was causing the nomenclature I wanted to override so I generated my own ivysettings.xml affecting those values only (note that I didn't replace the original ivysettings.xml):
<ivysettings>
<include url="${ivy.default.settings.dir}/ivysettings.xml"/>
<property name="ivy.local.default.ivy.pattern" value="[organisation]/[module]/[revision]/[type]s/[artifact]-[revision].[ext]" override="true"/>
<property name="ivy.local.default.artifact.pattern" value="[organisation]/[module]/[revision]/[type]s/[artifact]-[revision].[ext]" override="true"/>
<resolvers>
<filesystem name="local">
<ivy pattern="${ivy.local.default.root}/${ivy.local.default.ivy.pattern}" />
<artifact pattern="${ivy.local.default.root}/${ivy.local.default.artifact.pattern}" />
</filesystem>
</resolvers>
</ivysettings>