Thanks for your reply.
I can confirm that the used role has both of these permissions, but it still cannot amend those properties.
I can confirm that many of the other properties on the server can be amended, but not these, the GUI prevents us from amending these.
Is there something else that may be preventing their amendment?
To cut it down a bit, I've tried using a test role (and I've assigned it's permissions against our test server). It has these permissions on, so I can see the server firstly and then in theory I should be able to amend the properties.
With those permissions, I cannot amend the TRANSACTIONS_DIR or STAGING_DIR properties.
I have been informed that Server.Modify rights need to be given to the role. Thanks for your help anyway Siddu.