NIOS V: Systick based timeouts not available when using internal timer

Hi FabianL 

That issue that you are facing is valid and we are currently looking into it.

As a workaround currently could you try modify the generated alt_sys_init function to have the INTEL_NIOSV_M_INIT before the rest as shown below:

        void alt_sys_init( void ) {                    

                INTEL_NIOSV_M_INIT ( NIOS_SUBSYSTEM_INTEL_NIOSV_M_0, nios_subsystem_intel_niosv_m_0);

                ALTERA_AVALON_TIMER_INIT ( NIOS_SUBSYSTEM_TIMER_0, nios_subsystem_timer_0);    

                ALTERA_AVALON_JTAG_UART_INIT ( NIOS_SUBSYSTEM_JTAG_UART_0, nios_subsystem_jtag_uart_0);   

                ALTERA_AVALON_SPI_INIT ( NSC3_SUBSYSTEM_0_ADC_SPI, nsc3_subsystem_0_adc_spi);    

                ALTERA_AVALON_SYSID_QSYS_INIT ( NIOS_SUBSYSTEM_SYSID_NIOS, nios_subsystem_sysid_nios);    

                ALTERA_AVALON_UART_INIT ( NIOS_SUBSYSTEM_UART_IP, nios_subsystem_uart_ip);    

        }

For further details refer to the KDB :

https://community.altera.com/kb/knowledge-base/why-does-the-nios%C2%AE-v-processor-that-applies-fast-jtag-uart-driver-stop-stuck-in-/349481