So I have a good news, which could help all other members with similar problem. We had contacted Altera official technical support and we got reply which has solved our issue. I am pasting here the reply from support. Anyway, it was very hidden problem... almost impossible to solve with very deep knowledge of the Altera compilation processes and so on.
For your information, <installation>\ip\altera\sopc_builder_ip\altera_avalon_epcs_flash_controller\em_epcs_qsys.pm (line687) indicates that:
· CYCLONE and CYCLONEII will be using /ip/altera/nios2_ip/altera_nios2/boot_loader_epcs.srec
· STRATIXII, CYCLONEIVE and etc will be using /ip/altera/nios2_ip/altera_nios2/boot_loader_epcs_sii_siii_ciii.srec
· For V series device will be using /ip/altera/nios2_ip/altera_nios2/boot_loader_universal.srec
Thus, this can explain that rd11122013_865 is only applicable to Cyclone V (or V series) because different device is using different bootloader.
During my investigation, I found that Cyclone IV GX is missing from the bootloader check statement and this could be the cause of this issue.
Here, I would like to suggest a workaround as below:
Go to line# 703, <installation>ip/altera/sopc_builder_ip/altera_avalon_epcs_flash_controller/em_epcs_qsys.pm, add the device “CYCLONEIVGX” into the second condition check.
before:
($device_family eq "CYCLONEIVE"))
after:
($device_family eq "CYCLONEIVE") ||
($device_family eq "CYCLONEIVGX"))
I have also attached the modified em_epcs_qsys.pm file for your reference; you may compare and replace the file. The fixes of this issue will be included in ACDS 14.0. At the meantime, I have also file a KDB on this issue and the workaround will be publish soon.