This is an odd problem, and it's not even a real problem, it's just a minor annoyance. But I open this program many times a day, so it annoys me many times a day.
Every time I open PuTTY, the window opens on the left side of my desktop. Every other program will re-open in the same place it was when it closed. PuTTY always opens on the left (and in a slightly random position, too, which is also odd). I prefer my terminal windows on the right, and I have to open SSH windows 15+ times a day.
I'm on Windows 7. I have no idea if this is a PuTTY issue, a Windows 7 issue, or a combination of the two.
I thought maybe it had to do with how I'm closing the windows (usually by typing "exit" or "logout"). But closing them by clicking the red X has no effect either.