When i run a command in cygwin when scrolled up it starts writing the output to that screen, so everything gets written over. How can I change settings so that output will always be appended to the end not to where I have currently scrolled my window.
I found that rxvt doesn't do that but it also doesn't show me äöõü characters:(
Are you sure it's overwriting where you've currently scrolled to? I find the console just jumps back to the cursor position when there's new output. Still annoying though, and I don't know of a way to switch off that behaviour.
Anyway, have a look at 'mintty'. Like rxvt, it doesn't need an X server, but it does support Unicode, so the umlauts should be fine.