Pressing Ctrl-Pageup/down in PuTTY scrolls the scrollbar by 1 line. I wish to use this key sequence in vim. How do I disable this behaviour in PuTTY?
You can't, and even if you could disable it, it wouldn't help, because PuTTY doesn't support the keycodes for modifier key combinations with the cursor and function keys.
Perhaps there's a PuTTY derivative that supports those combinations. Mintty, the Cygwin terminal that's based on bits of PuTTY, certainly does support them, and it also allows the modifier for scrolling to be configured or disabled.