If it's a commonly reported problem, then I'd let it go.
I'd install another program to monitor the binaries as well, and as I'm the paranoid sort I'd go ahead and check the hashes of the binaries anyway -- it might be something to get done in a week or so though.
chkrootkit and rkhunter are not cPanel add-ons. They are stand-alone rootkit/malware detection apps which would have to be installed via SSH. However, it is good to have at least one of them installed on your server and to have a cron job set up so that your server is scanned daily for any malware.
I have heard of a tool called tripwire which is free and can keep track of binary file changes. But these binary files that register as possible trojans...what I would do is compare their checksum hashes with known good binaries from the same distro and revision...that will tell you if the binaries have been compromised or not.