I have been running Carbonite for about a year now on a 2007 iMac. I was running Lion at the start and now Mountain Lion. While still running Lion, I was able to reinstall everything without a problem after my hard drive slowly died earlier this year and was replaced by a new one.
I just noticed this morning while examining Activity Monitor that CarboniteDaemon continually was taking up anywhere from 65% - 120% of the CPU. After doing some quick research, I found this helpful post on another site:
"The high CPU usage problem stems from trying to backup running applications. The solution is to go to the Carbonite pane in System Preferences, select Backup and make sure that any folder that might contain a running app ("Applications", "devtools", etc.) is set to "Will not be backed up" (indicated with a red dot) next to the folder or file."
I followed that advice and it wasn't long until the CarboniteDaemon was back down to 0.3% as it should be. I hope this advice helps others as much as it did me.