I know this is fairly old, but in case anyone else stumbles across this problem...

Have a look in %LOCALAPPDATA%\VirtualStore, it's probably in there.

Vista introduced a new security feature that restricted permissions on Program Files directories and redirected file writes. Try starting WinSCP with administrative privileges (not ideal) or simply not transferring directly into Program Files.

I'm not sure that's the case, as the path to the directory that I'm browsing, has the (x86) suffix intact in the Program Files folder name.


Looking at this path:
C:\Program Files (x86)\Zend\Apache2\htdocs

That is the exact same path in WinSCP, and Windows Explorer.
Checking the 64-bit Program Files directory, there is no Zend folder at all.


Additionally, I use WinSCP in Win7 x64 all the time (I have for over a year now), and I've *never* seen this issue :-\

The computer this is occurring on, is not one of my own computers, so it could be something screwy in the OS, but without making that assumption, what I'm seeing just doesn't make sense.

Seeing that your Win7 is 64-bit my guess is that file system redirecting for 32-bit processes (WinSCP) is taking place.

So, working for a client, mirroring their web files from a remotely hosted windows machine, to a local windows 7 laptop.
The mirror/sync process hit errors where only 1 directory would not transfer properly.
To get around the error, I created a zip file of all files from the remote directory, downloaded it via FTP, extracted it.

Now when I attempt to view the file location in Win7, it says no files are there.


Specifics:
Installed Zend Server CE, w/ Apache, MySQL, etc, on laptop.
Installed WinSCP on laptop.
Connect to server, sync remote web dir down to local c:\Program Files (x86)\Zend\Apache2\htdocs\admin
Error is encountered, saying that a subdir (called js, containing only javascript files), cannot be transferred. Errors are on the file-level. Retried multiple times, works fine on other machines.

To circumvent error, RDP'd into remote machine, zipped up files, downloaded via WinSCP, extracted via WinSCP.
Then attempted to view directory via WinSCP, nothing there, the htdocs dir is entirely empty. Changes that I make in WinSCP, while remaining in WinSCP even after a reboot, do *not* show up at all in Win7 explorer view.

Weird, eh? I've never seen this before...