It's strange. I've been using WinSCP for almost a year on Win 7 (64bit) and it's been just fine. But about a month (give or take a week) ago that started happening to me.
I have sent you an email to address you have used to register on this forum.
Yesterday afternoon I went from the 4.x version to the latest 5.x version and I know one thing I did differently on install. Previously I always chose "custom upgrade" and this time I used "full upgrade" and the problem went away.
I tested on both Windows-FileZilla/FTP(over SSL) and Linux/SFTP and got good results both times.
Also the repeated loss/restore of connection only happens when connected to Windows server, so it is not a client issue.
I still think it was some problem caused by a Windows patch that started the initial issue, but by always using the custom upgrade I did not get to run the code that would have fixed it.
I should have replied with this information to your email last night. Sorry for the delay and thinks for your help!