Working on the SP2010 beta I bumped into an issue with search. I decided, after various attempts to fix it different ways, to rerun the Sharepoint 2010 Products Configuration Wizard. But when I did I ran into an error on Step #5 - namely a System.Security.Cryptography.CryptographicException of "Object Already Exists".

This was verified by checking the logs. I tried many, many things to resolve it, including making sure "Network Service" had full control over the 14-hive, per this blog and setting up Network Service using the aspnet_regiis -SampleKeys, etc. I even disabled the UAC (see my earlier post for an explanation).
No dice.
The resolution lay, as you may be suspecting, in messed up perms on the RSA folder, specifically C:\Program Data\Microsoft\Crypto\RSA\MachineKeys. I had checked to the RSA level and Administrators had full perms (I was logged on as with an Administrative account) but I had not taken the next step and checked MachineKeys.
Turns out that that folder had removed all perms from Adminstrators. I ended up having to take ownership of the folder and give Admins full perms again. Sure enough - it worked...
As a bonus it DID fix my Search problem (I was getting "The search request was unable to connect to the Search Service.").
Maybe.