Performance monitor reports and graphs don't show all the counters that were captured

I've run into an odd behavior of performance monitor that I haven't been able to clear up yet: after I run a data collector set, the resulting report only shows a partial list of the counters that I captured, and so does the graph of that report (but different
items).
For instance, I chose the following counters for the data collector set:
\PhysicalDisk(*)\% Idle Time
\PhysicalDisk(*)\Avg. Disk Queue Length
\PhysicalDisk(*)\Avg. Disk sec/Read
\PhysicalDisk(*)\Avg. Disk sec/Write
When the data collection ends, the report that gets displayed shows all those counters for _Total instance and C:, but then E: only shows % Idle Time and Avg. Disk Queue Length. That's it, the report ends there, even though I also have F: and V: drives on
this server.
If I choose to view the graph of this data collection, it only shows those four counters for the _Total instance.
It took me a while to realize that all the data is being captured, but it's just the display that is truncated. If I view the folder then open the report.html, it actually shows all the data. Same with the graphs. If I select to add counters and add
all the missing counters, they are displayed.
I have searched high and low but haven't been able to find more than one post at ServerFault where someone had a similar issue, but no real solution or cause was provided, so I was hoping that someone here might have an idea.
I also found a variety of articles about missing counters due to registry settings or because the counters needed to be reset, but that's a different issue that doesn't apply in my case. By the way, this is on a windows server 2012 R2 VM (file server).

Hi SomeAdmin,
The counter missing often caused by the related registry value is corrupted, please first refer the following related KB then perform a fix then monitor the issue again.
Event ID 3012 — Performance Counter Loading
http://technet.microsoft.com/en-us/library/cc775053(v=ws.10).aspx
More information:
Overview of Performance Monitoring
http://technet.microsoft.com/en-us/library/cc958257.aspx
PerfGuide: Analyzing Poor Disk Response Times
http://social.technet.microsoft.com/wiki/contents/articles/1516.perfguide-analyzing-poor-disk-response-times.aspx
Analyzing Storage Performance using the Windows Performance Analysis ToolKit (WPT)
http://blogs.technet.com/b/robertsmith/archive/2012/02/07/analyzing-storage-performance-using-the-windows-performance-toolkit.aspx
I’m glad to be of help to you!
Please remember to mark the replies as answers if they help and unmark them if they provide no help. If you have feedback for TechNet Support, contact [email protected]

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