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I have an SSD with ~125GB formatted, and it claims ~99GB are consumed. It has been rapidly consuming storage space for weeks. I have found many instances of unexplained SSD consumption online, none of which seemed to have my answer. 
My user's directory has been properly moved to another HDD with a junction so that none of my normal data storage is done on the SSD. Windows and Program Files are still present.
However, the strange thing is that I only have 46GB of data on the drive as confirmed by directory tree listings and Total Commander viewing hidden and system files. 
WinDirStat, manual inspection, and any other storage consumption analysis tool report 46GB of data on the drive when launched from a copy of Windows running on the SSD. 
This is a big discrepancy from the ~99GB consumed. Where is all my free space?
user1695505
Posted 2015-05-20T09:51:59.197
Reputation: 319
This is really not a question but an explanation of something I didn't find explained elsewhere before finding the answer myself. Please tell me if this doesn't belong here. – user1695505 – 2015-05-20T09:54:00.803
possible duplicate of How can I visualize the file system usage on Windows?
– Karan – 2015-05-20T09:54:49.2231@user1695505 Format it as a question then add the solution as an answer. Also add "answered" or "solved" to the title and accept your own answer. Then it is clear. – Ctrl-alt-dlt – 2015-05-20T09:55:45.323
1You need to run WinDirStat as admin so it finds everything. Also, as you've noted this is not a question at all. You could break this up into a question and an answer, but there are lots of duplicates on this very site and so it would get closed anyway. @JamieWilletts: No point really. – Karan – 2015-05-20T09:56:06.763
@Jamie Willetts - thank you, will do immediately. – user1695505 – 2015-05-20T09:56:21.957
@karan, this is not a duplicate nor a thread about using WinDirStat. This is a thread concerning free space that is consumed without apparent explanation while Windows is running from the drive. WinDirStat does not see the culprit folder at all when Windows is running from that drive, not even as admin. – user1695505 – 2015-05-20T10:06:59.880
Then one of the other tools listed in answers to that question will certainly find it. Also there are other questions dealing with the same system restore 'lost' data issue as well. – Karan – 2015-05-20T10:11:53.573
In my searches I did not find a clear answer to this problem, I found lots of similar problems with different answers. The folder in question is inaccessible while Windows is running, only something running at boot would be able to analyze the size of the folder in question. Moderators may feel free to remove this thread if they deem it a duplicate. – user1695505 – 2015-05-20T10:16:58.983
I was able to look at your intial scan and tell right away what was consuming your storage space. I was also going to point out you didn't run it with esclated privilages. – Ramhound – 2015-05-20T10:50:21.477
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@JamieWilletts: Please do not ask people to add "answered" or "solved" to the title. This is not a forum.
– Karan – 2015-05-20T17:21:28.9331@JamieWilletts: The way to do that on SU is to accept your own answer (need to wait 2 days after the question was asked to do that). – fixer1234 – 2015-05-21T04:08:19.907