eCos for Nios II 5.0 now available

This is the code in the .entry section, which is placed by the linker script at the reset address of the processor - which in your case would be a location in the EPCS device, not the SDRAM. Have you modified the linker script as well?

In any case, you can either just jump to the _start location instead, or if you really do need the code in the .entry section, you can remove the conditional compilation of this section (i.e. the use of CYG_HAL_STARTUP_ROM) in vectors.S.