Based upon the description, as well as the following error line, it appears that there may be an issue with the machine key:
RegisterWithoutCookie: Error 0x8009000d: class STWin32::CWin32Exception at X509Certificate.cpp:194: Error 2148073485: Key does not exist.
Was there an attempt to install the agent using insufficient credentials prior to this?
You can try the following:
1)Navigate to the following directory (depending upon operating system):
C:Documents and SettingsAll UsersApplication DataMicrosoftCryptoRSAMachineKeys
2) Open the first file in the list (using a basic text editor such as Notepad), and look for the clear text 'agent'. If you do not see the word 'agent' in clear text, move to the next file in the list.
3) Once you have identified the file containing the clear text 'agent' (this is the machine key for the agent software), delete said file.
4) Retry the agent installation.