Ok,
take a look within altera_sys_init() function placed within a file with same name and verify that is present ALTERA_AVALON_EPCS_FLASH_CONTROLLER_INIT call (that file is under BSP folder). If it is present take a look to where that macro is defined (altera_avalon_epcs_flash_controller.h) and verify that it is not empty; in that case (defined empty) it means that it is not satisfied following definition check:
#if (!defined(ALT_USE_SMALL_DRIVERS) && !defined(ALT_SIM_OPTIMIZE)) || defined ALT_USE_EPCS_FLASH
.
The use of small driver is selected within BSP editor.
Ciao