do you use a while(1) around read ???
you don't need an interrupt, this is always done in the HAL driver altera_avalon_uart.c
I don`t know if this is necessary, but set stdin,stdout,stderr in syslib properties to null or something other than
uart1.
int main()
{
fdterm = open("/dev/uart1", O_RDWR | O_NONBLOCK | O_NOCTTY);
fpterm = fdopen(fdterm,"rw+");
fprintf(fpterm,"UART1 STARTED\r\n"); // check initial output
while(1) {
uart1_rxcount=read(fdterm, &uart1_rxbuffer, sizeof(uart1_rxbuffer));
if(uart1_rxcount>0) { {
fprintf(fpterm,"received:%s\r\n",uart1_rxbuffer);
}
}
}