I have a similar problem trying to upgrade vCenter 4.1 to 5.x (tried both 5.0 and 5.1). Did you find a solution for your problem?
The pre-upgrade check tool sees the DSN and reads out the esxi hosts but then I get a connection error with no clear error message. The VMwareAgenUpgradeCheker log contains the following:
DSN64Accessor started successfully
[VCAgentU:QuickInf:W: 1] 2013-01-22 11:18:33.013 Virtual Center installed version :4.1.0.17435
[VCAgentU:QuickInf:M: 1] 2013-01-22 11:18:50.225 Error reading values from the registry System.NullReferenceException: Object reference not set to an instance of an object.
at PreAgentUpgradeChecker.Utils.RegUtil.RegOps.RegUtil_GetKeyValueData(RegistryKey hKey, String subKey, String keyValueName, Object& keyValueData)
[VCAgentU:Critical:P: 5] 2013-01-22 11:18:54.059 Connection State[]: Disconnected
[VCAgentU:SoapMsg :P: 5] 2013-01-22 11:18:54.067 Attempting graceful shutdown of service ...
[VCAgentU:SoapMsg :P: 5] 2013-01-22 11:18:54.072 Pending Invocation Count: 0
[VCAgentU:SoapMsg :P: 5] 2013-01-22 11:18:54.073 Graceful shutdown of service: Success
[VCAgentU:Error :P: 5] 2013-01-22 11:18:54.092 System.ArgumentNullException: Value cannot be null.
Parameter name: address
at System.Net.ServicePointManager.FindServicePoint(Uri address, IWebProxy proxy, ProxyChain& chain, HttpAbortDelegate& abortDelegate, Int32& abortState)
at System.Net.ServicePointManager.FindServicePoint(Uri address, IWebProxy proxy)
at System.Net.ServicePointManager.FindServicePoint(Uri address)
at VirtualInfrastructure.Soap.SoapServiceWrapper.Dispose()
[VCAgentU:Critical:P: 5] 2013-01-22 11:18:54.093 Connection State[]: Disconnected
....
I have tried to resolve the issue by upgrading SQL2005 32 bit to SQL2008 32 bit, then to SQL208 64bit. But that didn't resolve the problem.
Tried to run upgrade checker as administrator, VJ# and .NET 3.5 are installed.