ATMEGA328 Serial input via ISR to buffer - buffer messed on printout
You have a few problems here.

strcmp compares 2 null terminated strings, but you are using it to compare usart_input_buffer (which is not null terminated) with a character '\r' which is also not a null terminated string. Try 

if(usart_input_buffer[usart_in_count] == '\r') {


Also, to make a string null terminated you have to add the terminating null yourself. Like this:

if(usart_input_buffer[usart_in_count] == '\r') {
    usart_input_buffer[usart_in_count+1] = '\0';
    usart_in_count = 0;
    usart_valid = 1;
} else {
    usart_in_count++;
}