I run as a standard account on Vista Ultimate. The installer needs admin privileges so that it can update c:\Program Files. As a result, the installer ran under my administrative account. When it shut down, updated the Hotsync conduit and restarted Hotsync, Hotsync was running under my admin account. This means that all Hotsync data ended up in the wrong user directory structure. Also, the conduit was looking in the wrong place for PDFs to be uploaded to the Palm. Restarting Hotsync under my standard account did not work - the Adobe Reader conduit did not show up in my Hotsync settings.
The solution was to change my standard account to have administrative privileges. I also installed Adobe Reader for Palm to a different directory, rather than under c:\Program Files - I am not sure this is required but has been recommended for other applications that are not Vista-compliant. The Hotsync conduits were properly updated this time but would not automatically restart - a manual restart was successful. I was then successfully able to sync PDFs.