So I performed a replication of IIS from an old server to a new server (IIS 6.0 to IIS 7.5 being the current new server). I've copied over all of the sites and virtual directories. I can FTP and DIR on all of the newly copied virtual directories and sites except for one, however it works perfectly fine on the old server.
New server
230 User logged in.
Remote system type is Windows_NT.
ftp> dir
200 PORT command successful.
550 Keyset does not exist
ftp> cd xxxxxdir
550 The system cannot find the file specified.
ftp>
Old server
Remote system type is Windows_NT.
ftp> dir
200 PORT command successful.
150 Opening ASCII mode data connection for /bin/ls.
02-16-11 08:42AM <DIR> xxxxdir
09-16-13 07:48AM <DIR> xxxxdir
09-16-13 07:51AM <DIR> xxxxdir
09-16-13 07:50AM <DIR> xxxxdir
226 Transfer complete.
202 bytes received in 0.0013 seconds (153.98 Kbytes/s)
ftp>
I've read around that it was a permissions issue with a file in C:\ProgramData\Microsoft\Crypto\RSA\MachineKeys\xxxxxx but it didn't seem to fix the problem.
All permissions and authorizations are exactly alike between the old and new servers.