Solution for Programmer problems on 64 bit windows in Quartus 12

Yes, this is utterly lame.

Can I make a small suggestion though. Rather than installing files from a random zip file it may be safer to install the 64 bit programmer install and use the files from there. (It's not that I don't trust you, but it's probably bad practice to install files pointed to from forum posts)

I would also recommend that you specify a full path to jtagserver.exe when installing it - I often see issues where the wrong jtagserver.exe has been installed because the path has been set up wrong. The commands would be:

jtagserver --uninstall
c:\altera\12.0\quartus\bin64\jtagserver --install
jtagserver --start

(Technically you shouldn't need to start it as the debug tools will start jtagserver automatically if it is installed but stopped, but it doesn't hurt)

With any luck the 12.1 release will do a better job.