I have a brand new windows 2012 standard server, with the gui installed and I have mounted three volumes from a storage array onto the C drive under another folder. So I have folder "A" setup on the server, and three junctions inside that called "B", "C" and "D", each of which is linked to a 3TB set of discs. I used the File and Storage services gui to setup these junctions, and they appear to function perfectly within the server itself. The drives appear as reparse points within the explorer interface(So the drive icon with the arrow).
Now the issue comes when these are used on client machines, and the same goes for XP, 7 and 8, but not osx. The junctions appear as a shortcut(So a folder icon with an arrow), and can be clicked on but when you come back into folder "A" to look at the links the junction you just entered is gone. The same goes for all three junctions, and is only fixed by closing and re-opening explorer after a seemingly random amount of time.
After some fiddling I discovered that the link icon is disapearing and being replaced with a folder that is marked in file explorer as being either hidden or system(Although checking in a command prompt says no such thing, the folders are clearly marked as Reparse points and are not hidden or system). This makes it even more confusing when turning on "view hidden, system...etc" in windows explorer makes those folder appear in their slightly faded form(As if they are system or hidden). Closing and re-opening explorer returns these folders back to their original state temporarily.
I've fixed it in the sort-term by turning on the show hidden option in explorer, but this is not a long-term solution as it is causing lots of issues for users who are having to deal with thumbs.db issues and similar things. Has anyone come across this?