I tried un-installing and re-installing but still no joy. I did in fact select the full install on the first occassion and made sure that all options were selected and also that all would run from disk.
To resolve the issue I manually created a new website at the same level as the 'Default Web Site' which is used by the other QV components. e.g. QVPlugin, QVjava etc.
This new website was set-up to use port 4780. I called this website QVAdmin although the name doesn't really matter.
Next three virtual directories were created under the new website. QEMC, QMC & QMCCommon and these all mapped to the appropriate directories under;
C:\Program Files\QlikView\QlikView Management Service\
The authentication method on the website and virtual directories was se to 'Integrated Windows authentication' only.
Then via the IIS management snap-in select Home Directory tab > Configuration > Options and ensure that Enable Parent Paths is checked.