> Now here's something I don' understand yet:
>
> ZTree finds _54_ "junction directories" -- but I've also run three
> (3) other programs that "agree".. They indicate that my same Windows 7
> has _46_ junctions (...where two are the "non-Windows junctions").
>
> So is it 46, or 54 junctions...?
>
> The three programs that list 46 junction points, are:
>
> 1) NTFSLinksView 1.16 x64 (portable) - from Nirsoft:
> http://www.nirsoft.net/utils/ntfs_links_view.html
>
> 2) Junction 1.06 (command line) - from Sysinternals:
> https://technet.microsoft.com/en-us/sysinternals/bb896768.aspx
>
> 3) the "Repair Reparse Points" part of "Tweaking.com - Windows
> Repair":
> http://www.tweaking.com/content/page/windows_repair_all_in_one.html
>
> ( The last one definitely produces the best "output display" (chart
> with columns), if you want a nice screenshot. Also, the one from Nirsoft
> will save a tab-delimited text output. The output of Junction from
> Sysinternals is "ugly", but all three programs give the same list of 46
> results.)

OS = Win7 Enterprise SP1, fully patched

Sysinternals' Junctions v1.06's output was so "ugly" that I decided not to use it. Nirsoft's NTFSLinksView v1.16 was clear and appeared quite useful, so I decided to use it.

NTFSLinksView produced 94 junctions from C:\ on my system, of which 4 were identified as symbolic links. By my previously described process, ZTree produced 97 junctions from C:\ on my system, without distinguishing any of them as symbolic links.

To identify the differences between the two outputs, first, I saved NTFSLinksView's output to CSV and converted the Full Path output to an alphabetized text file via Excel and TextPad. Next, I compared that file to the alphabetized text file I produced from batch filing the ZTree output on all directories tagged with the "+J" attribute, as previously described. Using WinMerge or UltraCompare, the differences emerged. They were:

NTFSLinksView identified the 4 symbolic links as

NAME | FULL PATH | TYPE | TARGET PATH
All Users | C:\Users\All Users | Symbolic Link | C:\ProgramData
java.exe | C:\ProgramData\Oracle\Java\javapath\java.exe | Symbolic Link | C:\Program Files (x86)\Java\jre1.8.0_77\bin\java.exe
javaw.exe | C:\ProgramData\Oracle\Java\javapath\javaw.exe | Symbolic Link | C:\Program Files (x86)\Java\jre1.8.0_77\bin\javaw.exe
javaws.exe| C:\ProgramData\Oracle\Java\javapath\javaws.exe | Symbolic Link | C:\Program Files (x86)\Java\jre1.8.0_77\bin\javaws.exe

ZTree did not recognize the last three, but as it turns out, that's because they are files and not directories. If after fully logging the root of the disk I had remained in File Mode in ZTree, and then tagged all files with the "+J" attribute, I would have gotten the three java links above.

ZTree identified 6 junctions that NTFSLinksView did not pick up. They were:

C:\Users\All Users\Application Data
C:\Users\All Users\Desktop
C:\Users\All Users\Documents
C:\Users\All Users\Favorites
C:\Users\All Users\Start Menu
C:\Users\All Users\Templates

So to summarize, there were 91 junctions common to both methods. NTFSLinksView found three file-based symbolic links that ZTree wouldn't find in Dir Mode, and ZTree found six junctions that NTFSLinksView didn't find. All is now reconciled.

Hope that helps explain a method to analyze your system.