It looks like a bug may have been re-introduced into Dynamics 365 Server, v9.0 (on-premises) Update 0.28.
In update 0.9, there was a problem that was fixed and described as:
An error intermittently occurred when attempting to install Dynamics 365 ("...Could not acquire Write lock in time 30,000 milliseconds...").
I have been working on a number of on-premise deployments over the past few weeks and have been slipstreaming the cumulative updates during our installation. 0.26 and 0.27 have been working well. We switched to using 0.28 earlier today and the deployments are now failing. Without making any change, other than which cumulative update is applied, the problem is resolved.