After browsing a bit more I noticed that posting the debug 3 usually helps so here it is:
Status: Connecting to www.***********.edu
Trace: Going to execute "C:\Documents and Settings\sichn\Desktop\FileZilla-3.3.3\fzsftp.exe"
Response: fzSftp started
Trace: CSftpControlSocket::ConnectParseResponse(fzSftp started)
Command: open "*****@www.**********.edu" 22
Trace: Looking up host "www.*********.edu"
Trace: Connecting to 188.8.131.52 port 22
Trace: Server version: SSH-2.0-1.82 sshlib: WinSSHD 4.23
Trace: Using SSH protocol version 2
Trace: We claim version: SSH-2.0-PuTTY_Local:_Jun_13_2010_23:53:51
Trace: Doing Diffie-Hellman group exchange
Trace: Doing Diffie-Hellman key exchange with hash SHA-1
Trace: Host key fingerprint is:
Trace: ssh-dss 1024 44:c3:ad:77:fc:f4:4f:38:13:1d:a4:e9:10:63:60:00
Trace: Initialised AES-256 CBC client->server encryption
Trace: Initialised HMAC-SHA1 client->server MAC algorithm
Trace: Initialised AES-256 CBC server->client encryption
Trace: Initialised HMAC-SHA1 server->client MAC algorithm
Command: Pass: **********
Trace: Sent password
Trace: Access granted
Trace: Opened channel for session
Trace: Started a shell/command
Status: Connected to ***********.edu
Trace: Server sent command exit status 3
Error: Connection closed by server with exitcode 3
Error: Could not connect to server
Status: Waiting to retry...
I also found another thread detailing this same problem with an exit code 1 and he described not having shell access set correctly (I think). Could this be my problem, and if it is is this something that is fixed client-side or server-side?