I have two instances on one of my servers, and when installing service pack 3 the GUI installer does not recognize one of the instances. Server is Windows Server 2008R2 Enterprise x64 SP1
Both instances are standard edition 64 bit, both instances are named.
Before attempting the service pack one instance was 10.50.4033 and the second instance was 10.50.4000. When only the first instance appeared I went ahead and applied the service pack successfully, restarted, and ran the installer again hoping the second instance would appear miraculously. It did not. I am local server admin, sysadmin, all that jazz. I attempted to run the installer as admin, no luck.
I have scoured the SQL Server logs, application logs, system logs, and can't find anything that would point to why it is not picking up the second instance.
What next? Why is the installer not recognizing the second instance? Where else can I look for clues?
EDIT: Results for Kin's TSQL script
PhysicalMachineName servername SQLServerName servername\instance1 ServerEdition Standard Edition (64-bit) ProductVersion SQL Server 2008 + SP3 + (Build 10.50.6000.34) O.S. Windows NT 6.1 <X64> (Build 7601: Service Pack 1) (Hypervisor) Collation SQL_Latin1_General_CP1_CI_AS PhysicalMachineName servername SQLServerName servername\instance2 ServerEdition Standard Edition (64-bit) ProductVersion SQL Server 2008 + SP2 + (Build 10.50.4000.0) O.S. Windows NT 6.1 <X64> (Build 7601: Service Pack 1) (Hypervisor) Collation SQL_Latin1_General_CP1_CI_AS
EDIT 2: The installer logs show that it is recognizing both instances and all shared features. In the User Input Settings it shows ALLINSTANCES: False
EDIT 3: The details log led me to KB969052 and the script that comes with it has revealed several missing .msi files. Going to attempt to fix that and see what happens.
EDIT 4: created all the missing directories and moved copies of the .msi files from the installer cache and ran the update again. Nothing. Just shows grayed out boxes for the one instance already at SP3 and the shared features.
I even ran the Windows Installer Cache Verifier Package from Microsoft to check if the installer cache had been compromised. No errors or missing files were found.
This is a test system, and on a lark I checked the prod setup. Found the same thing. Main instance at 10.50.4033 and second instance at 10.50.4000, attempted to run the SP3 installer and it only recognized the main instance.
Both servers show that at some point in the past KB2977320 Security update for SP2, which would brings the instance up to .4033 failed to install. I am going to assume the failure is on the second instance for both servers. Downloading the KB and attempting to run the GUI also fails to recognize the second instance.
EDIT 5: I am officially perplexed. The setup bootstrap logs for the instance that the x64 installer recognized are in the C:\Program Files directory. The setup bootstrap logs for the instance that was not recognized by the installer are in the C:\Program Files (x86) directory. I tried the x86 installer and it recognizes the second instance although it fails to upgrade the instance.
This is a standalone database server built for one specific vendor application because they were being difficult, and it has been plagued with problems from the start. I would not be surprised if half the problems I have come to SE with have been because of this application. At this point I am going to assume the vendor has done something in the past that is causing this and leave it where it is. The problematic instance also shows up under the Wow6432Node registry keys for what it's worth.