This is a issue that has been submitted to Microsoft connect.

The documentation states the resource database and the master database must be in the same folder.

What it does not say is the resource database log file must be in the master database folder.

So if you put log files on one disk and database files on another disk the install will fail unless you put a copy of the resource database log where the master database data file is. After it is updated you can just copy it back to the log file location and all is well.