Hi Guys – I figured out the issue from my side and on my server this all relates to permissions and users.
1. I changed /wp-content/ (and all directories below that) to have full write permissions (i.e. 0777).
2. I changed my owner and group permissions for the /plugins/ and /upgrade/ folders to the same as my apache owner and group. In my case my apache user is www-data and the group is also www-data.
Once I changed these two things my upgrade functionality worked perfectly.
