Nope, you're not done checking your hard drive. You're getting some bad advice. This applies to chkdsk, surface scan, error checking, etc. when you select the options to recover bad sectors. There are two things that may happen here:
1) When you get the message "volume clean" it ONLY means it checked that small area on your hard drive called, "system reserved". And when you hit a key, it boots normally, but you have NOT done a surface scan or checkdisk. The key here is that it happens within seconds of your reboot.
2) If your chkdsk briefly shows it's checking and then quickly goes to a normal boot, it actually repaired or cleaned the area in system reserved.
In either of the two instances it did not do a full check on your disk. It needs to have a clean system reserve to save data while it does a full scan.
Once one of the two items above has been noted, you need to once again do a chkdsk, and you will find the normal one or two hour scan. Most people don't notice the two items above because they have to be watching the screen... usually they start the scan and walk off.
What I can't answer is why sometimes it will halt so to tell you the area is clean. I have some guesses, but they are probably wrong.
Regardless you need to run it again and expect it to run for a long time. I also might add, that "sometimes" but very seldom, it does a partial clean and requires you to clean it again. There is no prompt telling you this, as what you should be doing, and most people don't, is go into the Administrative Tools and then find the Event Viewer and look at the results of the scan from the "Application Log" of the event viewer. You search for the latest "Wininit" log and read it.
The bottom line if you see the words, "volume clean" you have fixed NOTHING. You need to run it again. This app, regardless what Microsoft calls it with each version is not fully automatic and takes a little work on your part to be sure you performed a good surface scan of your hard drive.
1It means that no errors are present in the file system. – Paul – 2015-12-10T22:11:58.007
@Paul - How come it never popped up before? Just this time? – None – 2015-12-10T22:21:27.307
What "check disk" software are you using, and what is the filesystem on the disk being checked? – Paul – 2015-12-10T22:25:16.060
Windows 7 64-Bit, NTFS, and I run it from cmd using /f /r – None – 2015-12-10T22:35:04.043
Clean means that no errors were found, are you saying that normally you have errors reported? Can you run it again and show a screenshot? – Paul – 2015-12-10T22:58:43.027
No, normally I don't get errors. Let me elaborate. When I usually run check disk, it runs,finishes and reboots and goes to the login screen. This time however, when it rebooted it said "The volume is clean". Normally it never did that before. Not a problem, just wondering why all of a sudden that message appeared. – None – 2015-12-10T23:02:07.760