Originally with Windows 8.0 I hadn't had any issue while using programs such as putty, winscp, filezilla, etc. Ever since upgrading to Windows 8.1 I have run into more and more issues with these programs. For instance, putty will just randomly disconnect, winscp is unable to transfer any files (more than a few seconds, and then it disconnects) and the same goes for filezilla.
I have done some troubleshooting, involving trying to connect to other remote machines from the laptop that is experiencing the issues, tried different NICs (Wireless and Wired), used different networks, called up our ISP support, reset winsock, reset Windows Firewall, Re-installed drivers. I have troubleshooted with the dev of winscp and he came to the conclusion that the issue is the OS on my laptop, not the program, and not the remote machine.
I am not sure how else to troubleshoot this issue short of re-installing Windows and I don't have the time to do that as a Student. Unfortunately, ssh is a heavy part of my school work (majoring IT). After going on several forums, and no one being able to address the issue to solve this, short of telling me that something is wrong with the networking stack on my laptop, I need someone to help me address this issue.
I have posted this in the forum of the software vendor. We went through some detailed troubleshooting processes, and tried multiple computers. The only one that experienced this issue was the Windows 8.1 laptop that I am using right now.
I have ran the troubleshooting tool in the Action Center, on Network Adapters though, since I am not having a problem connecting to a website.
I did check that yesterday to make sure that I wasn't missing anything. The only two updates I a missing are "optional" bing and silverlight updates (I know one of them for sure was bing, the other was something similar). All required updates that don't add software/bloatware like that are installed.