SQL Server 2008 R2 Agent only see's 40 processors

Where do you "see" that in "SQL 2008 R2 server agent"??
Can you post a screenshot?

Run Windows Updates & update the system Bios and drivers.

Also - Is "Hyper-Threading" enabled on that computer? I suggest disable it if only SQL is running on it.

"A hyper-threaded CPU introduces common CPU cache invalidation issues that physical multiprocessor implementations do not experience. The application workload can affect the performance gains and the common CPU cache behavior."

http://support.microsoft.com/kb/322385

And lot more food for thought about hyper-threading here:

"•Turn off hyperthreading if the logical CPU count that would result exceeds the number of CPUs supported by your OS or other software.  Example: Windows Server 2008 R2 supports up to 64 logical  processors, If you have a 40 core server (4, 10 core processors) hyperthreading would result in 80 logical cores. This is 16 cores greater than the OS will support. At start up those 16 logical cores will not be initialized and will be idle.  That is 8 physical cores of processing power not in use."

http://blogs.msdn.com/b/sqladventurer/archive/2012/07/11/hyperthreading-turbo-boost-sql-server-and-you.aspx

http://sqlblog.com/blogs/joe_chang/archive/2013/04/08/hyper-threading-performance.aspx

lcohan,
Here is the screen shots below
SQL3.jpg
SQL4.jpg

Can you please try run commands below in your SQL SSMS? It may be the difference between virtual/logical processors I mentioned about:

-- Identify Virtual Processors
SELECT cpu_count
FROM sys.dm_os_sys_info
 GO


SELECT cpu_count AS [Logical CPU Count], hyperthread_ratio AS Hyperthread_Ratio,
cpu_count/hyperthread_ratio AS Physical_CPU_Count,
physical_memory_in_bytes/1048576 AS Physical_Memory_in_MB,
sqlserver_start_time, affinity_type_desc -- (affinity_type_desc is only in 2008 R2)
FROM sys.dm_os_sys_info

If this is running on a server, please post the brand and model

We aren't running hyper threading on this server.

Here is the results of the query.
3-26-2014-1-10-05-PM.jpg

Does MAXDOP have anything to do with this?  Its currently set at 4.  Should this be changed to 8?

Anyone know?  Please?

What is the SQL Server Service pack and what is your SSMS Service pack from where you run these GUI "properties"? SSMS needs SQL Service pack to be applied as well...

Microsoft SQL Server Management Studio  -  10.50.4000.0
Microsoft SQL Server 2008 R2 - 10.50.4000.0

our bigger issue is why does the sql agent only acknowlege 40 processors when sql server acknowledges 80

Is there a CU that fixes this issue?

I personally never heard to be honest and never seen such thing like in your screen shots (I checked ALL servers I have access to and they all show the exact same number in the two places from your screenshot) and I suggest you post the same question on MSDN support/forums.

http://msdn.microsoft.com/en-us/hh361695.aspx

Thanks lcohan.  I posted that question on that forum.  I hope we can get an answer soon.  May I ask if your running any CU packages on your SQL servers?  I saw there is about 12 of them for SP2.  I'm curious if any of those address this issue.