If you're using the VC Office add-in and finding that the first email in a conversation indexes into VC correctly but subsequent replies don't, this is typically a server-side issue that will need investigating by a support technician. The same applies to subject and address-based rules for the CCMail for Exchange service, though in these cases even the first email may fail to index, not just the replies.
For conversation rules specifically, everything after the first email is captured via the Virtual Cabinet Capture service on the server. Similarly, for CCMail/subject+address rules, all replies are processed on the server via the CCMail for Exchange service. As a result, any configuration of these services, or checks on email journaling/transport rules, will need to be carried out by one of our technicians alongside your IT support.
To help speed things up, please email your IT support/host to authorise our server access, and send us the ticket number once you have it.
We'll then contact them directly, investigate the issue, and update you once we have more information.