Hi, I had the same frustrations and I found a Windows XP registry setting that I believe changes the keyboard mapping of the right alt key to be the same keyboard code as the left. Whatever it does, my right alt key now acts exactly like the left one in PuTTy on Windows XP. It might screw you if you want to use the right alt key as AltGr in the future. I dont think I care so it's okay with me.
Here's the page I got the registry hack from:
http://keyboards.jargon-file.org/
At the very bottom is a link called "menu.altgr.reg". Download that and run it, then reboot your system. PuTTy should work the way you want.