When you upgrade Adobe Reader from 9 or 10 (X) to 11 (XI) you may be prompted “Trusted certificates from your previous version of Adobe Reader were found. Would you like to import them?” To avoid this prompt you can add two registry keys that will automatically import the trusted certificates the keys to set are as follows:
HKEY_CURRENT_USER\Software\Adobe\Acrobat Reader\11.0\Security\cDigSig\cAdobeDownload
bAskBeforeInstalling REG_DWORD 0x1
bLoadSettingsFromURL REG_DWORD 0x0
There was some documentation that mentioned you may need to set the key iCheckEvery but in my testing it was not necessary.