A screenshot from TreeSize would be VERY USEFUL to compare with WizTree.
Wiztree is very quick because it gets all its data from the MFT,
but is therefore not suitable for FAT32 format.
TreeSize is slower - I guess because it trawls through directory structures.
When I scan Partition R:\
Wiztree IMMEDIATELY shows
Total Space 742.2 GB
Space Used 736.4 GB
Space Free 5.8 GB
Then it spends less than 4 seconds scanning the MFT,
and a further 3 seconds preparing the "Tree View" which lists the folders, sizes, and numbers of files.
This is when I see a maximum total of 316,004 files in R:\
TreeSize Free takes 10 seconds building up totals,
During that time its total size for R:\ gradually creeps up to 735.9 GB.
It only sees 315,986 files
TreeSize is unable to see the folder R:\$Extend\ or the 8 files which WizTree reports
WizTree also sees and reports these 9 files, which TreeSize also ignores
the 436.8 MB file R:\$MFT
and 8 more R:\$etc files that total 100 MB
My guess is that WizTRee and WinDirStat are telling you the same thing because they both use the MFT.
If Windows Explorer properties and TreeSize agree that C:\ has about 576,000 files your problem might just be an error in the MFT entry that states the Free Space.
If Windows Explorer properties and TreeSize indicate a vastly different quantity of files then the MFT could be horribly corrupt.
IT IS POSSIBLE THE MFT IS CORRUPT,
Otherwise there would not be a backup/repair mechanism which I believe involves $MFT and MFTMirr,
and hopefully there are experts here who know the relevant procedures and magic spells.
I am not sure of the prudence of :-
attempting to detect and remove malware files if you are accessing it via a corrupt MFT;
or of attempting to investigate and maybe repair the MFT in the presence of a RootKit
That is a question to ask at any malware fighting forum.
@ICit2lol
Sorry, I do not see any reason to suspect malware, but perhaps you have seen this sort of problem before.
I would have thought the "Healthy OEM" partition to be common when a P.C. is supplied with Windows pre-installed,
and having a separate partition for a Pagefile is fairly common
(though it is a beginner's mistake to have it on the same Drive as C:\)
I am surprised that C:\ is marked as Active instead of the 200 MB partition at the start of the Disk.
Regards
Alan