I ran into this issue with Performance Monitoring. Counter sets for an agent were not responding and they were listed in PerfMon. I tried running KaseyaMonitor.lua which return the following error when attempting to create the counter sets, "The parameter is incorrect. The counter is already active." What I found was there were references to the counters in the registry under the following keys:
HKLM\Software\Microsoft\Windows NT\CurrentVersion\Schedule\TaskCache\TasksHKLM\Software\Microsoft\Windows NT\CurrentVersion\Schedule\TaskCache\Tasks\tree\Microsoft\Windows\PLA
After backing these keys, I searched and manually removed each reference containing KCTR$. Once removed, I ran "lua.exe AgentTempDirectory\KMonitorSets\KaseyaMonitor.lua AgentTempDirectory" and the counter sets were recreated without issue. This was an odd issue to say the least.
I have had this exact problem off and on for several years. It has bit me on several occasions. I have found that often times running update list by scan corrects the problem and other times removing and re-assigning the monitor set helps.
I have spoke to many folks at Kaseya and opened feature requests for some sort of automated check to find if the monitor is not working. There was one or two folks that shared some things that were planned to be implemented to help, but those folks are no longer with Kaseya, so I don't know what the status is.
Take a look at this thread: community.kaseya.com/.../19060.aspx
Not an automated solution but a step in the right direction to see what monitor sets are not returning data.