I am experiencing the same problems (zero in rx fifo) I think I have found an error in one of the pm files named: "em_fifoed_uart_qsys.pm", I think this typing error is causing receive fifos to be disabled even if you enable them...
...# enw for fifoed uart
$use_tx_fifo = $Options->{use_tx_fifo};
$use_rx_fifo = $use_rx_fifo;
$hw_cts = $Options->{hw_cts};
$trans_pin = $Options->{trans_pin};
$fifo_size_tx = $Options->{fifo_size_tx};
$fifo_size_rx = $Options->{fifo_size_rx};
...
I think the line "$use_rx_fifo = $use_rx_fifo;" has a typing error, but when I changed it as "$use_rx_fifo = $Options->{use_rx_fifo};", I cannot make qsys generate the files. It freezes while creating the files.
Thanks for any help...