Windows Disk I/O 100% at boot for 20 Minutes

I have a fast computer (quad-core i7, 3.5 Ghz, 24 GB of RAM, Windows 8.1) and I installed a new hard drive less than a year ago that was supposed to be as fast as you could buy for an HHD and not an SSD.

On boot, the computer is extremely slow for about 20 minutes (literally 20 minutes). Nothing will load. Opening programs will just hang.

Went into Resource Monitor and found that my disk I/O is at 100% that entire period. In fact, it looks like one program is just going to town on my disk: CompatTelRunner.exe. I've Googled it, but there are hardly any results, so I don't know what service this is.

Here are some screen shots at 5 and 10 minutes in:

It could be a hard drive issue (Windows 8.1 Update 1 Disk Usage 100%), but HD Tune shows burst rate at 22.8 MB/s and average around 81.0 MB/s

You can disable the scheduled tasks that starts CompatTelTunner.exe by looking in the Task Scheduler.
Computer Management – System Tools – Task Schedule Library – Microsoft – Windows – Application Experience
or
Start - Run - taskschd.msc
Name: Microsoft Compatibility Appraiser
Location: \Microsoft\Windows\Application Experience
Collects program telemetry information if opted-in to the Microsoft Customer Experience Improvement Program.
Right click on “Microsoft Compatibility Appraiser” and select “Disable” By default, it is set to start if there is ANY network connection.

The executable is located here: C:\Windows\System32\CompatTelRunner.exe

You may also want to look at the following:
Customer Experience Improvement Program states

If the user has consented to participate in the Windows Customer Experience Improvement Program, this job collects and sends usage data to Microsoft. However, it is set to run even if opted out
Siuf (under Feedback)

Short answer: it's "legitimate" disk usage by a MS tool, just like the MsMpEng (MS Malware Protection Engine) it's scanning your disk regularly.

How do I get to that statement? Well, I have had the same behaviour on my Win 7 machines and did some digging. First, I used the Resource Monitor and found CompatTelRunner.exe reading what looked like all of my disks/files, like e.g. a malware scanner does. During that time it was also writing to a directory ( C:\windows\temp\compattelemetrylogs ). When it was done with the disk work, it started showing network activity on the upstream (matching what is mentioned in an Avast Forum Entry). I checked the above directory and found confirmed what the file and directory names hint at: it seems to be "Compatibility Telemetry Information". That means that MS seems to be scanning all PCs that have the update installed (i.e. all that are Win10-compatible), collecting information about all installed programs and features (read: about "everything"), and then sends at least part of that information or a status report to MS servers (I have not network-screened it... yet).

The frequent re-releases of the update can mean many different things, like compatibility updates, scan rule updates, anything, really. However, I don't like that MS scrapes all of my machines (and everyone else's, too) for information and does not tell me about it. Even if that information may be helpful or even necessary in providing the seamless upgrade path to Win10.

If you don't want to go to Win10 on that machine, you should consider removing the upgrade.

I had this issue also (I'm on Windows 7, but the issue is identical). Many sources have found that KB2976978 has been re-released numerous times; it's likely that the version of the patch you have is an older release with glitchy behavior. Uninstall it from appwiz.cpl and reboot. Windows Update will re-offer it next time it checks for updates. I went ahead and reinstalled it and everything seems fine now.