Did you remember to stop the vCenter server service? Also if you are using windows 2008, make sure to run the command prompt "administrator" if you aren't log on as the local administrator.

Did you find a resolution to this issue?  I have exactly the same scenario here.

We eventually raised a support call on this.  The support guy said it was a known issue and that they are working to resolve it.  He did not have any details on the possible cause of the issue, but we have a hunch (our hunch, not VMware) that that it may be something to do with the database having been upgraded to 4.0 from the original 3.5 installation.

Although no fix was offered, we didn't need it - the data migration method was not applicable to our upgrade (vCenter 4.0, 32-bit on a physical server backed by SQL 2005 Express -> vCenter 4.1, 64-bit on a virtual server backed by SQL 2008 Standard).  We had to migrate the databases manually before running the 4.1 installer and pointing DSN to the new database.  We also had to manually copy the certificates from the old to the new server.

Although this does not answer the original problem, there is a way around it.

hooch1964,

I actually have to perform the exact same upgrade.

(vCenter 4.0, 32-bit on a physical server backed by SQL 2005 Express -> vCenter 4.1, 64-bit on a virtual server backed by SQL 2008 Standard).

Could you possibly e-mail me your complete list of steps that worked for you?  dornfm94 -at- hotmail -dot- com.

Thank you,

Matt

Hi, I am out of the office, returning on Monday 6th June and will answer your query on my return.