Nios-II SOPC UART delivers wrong bytes

Also try out Bray terminal (I'm guessing you are using hyperterminal). I have heard of issues with uart buffer flushing on the PC side as well. When you say that you read 2 instead of 4 are you sure you are triggered properly? (i.e. sampling before the shift operations are complete). This could be any number of problems so until you get more help from us we need some more information (how you set up the uart, flow control?, baud rate, what you have on the host side, etc....). Also so that we are on the same page here, which direction are you referring to in your posts? (sometimes it sounds like tx and other times it rx)