I have found the solution to the problem. It seems to be a bug in VMware, but can be caused by group policy settings, that enable auditing. It appears to happen if you have a virtual machine, add it to your domain, and after that, add another drive such as D or E to the virtual machine.

My solution was to turn off the following GPO setting that was applying to the server -

    Default Domain Controllers Policy, go to Computer Configuration > Policies > Windows Settings > Security Settings > Local Policies >Audit Policy
    Audit object access
    Define these policy settings
    This was set, I unchecked it, so it is now Not Defined

Once the GPO was updated I rebooted the server twice, to apply the settings. and the access errors about not connecting to D drive disappeared. Another way of testing the problem is to try and access the administrative share of the drive, for eg \\server\d$. You will get an error about access denied. Once the GPO is turned off, the administrative share will work.

It is related to the VMware hot plug of drives http://kb.vmware.com/selfservice/microsites/search.do?language=en_US&cmd=displayKC&externalId=1012225, I haven't tested this though.