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I have a question, my C code is loaded in external RAM now (when I use JTAG), do I need a bootloader included in NIOS? if yes, how?
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Yes, you need a boot loader. Although, it sounds like you already have one. The EPCS controller in SOPC builder includes a small amount of block RAM which contains the boot loader. This is why you should set your reset vector to point to the EPCS controller.
Although, as I mentioned before, none of this should have an impact on the FGPA configuration itself loading.
Unfortunately, I don't have many other ideas for things to try. I have always had good luck with configuring from EPCS so I have not had to do a lot of troubleshooting myself. Perhaps monitoring some of the status signals or checking the communication to the EPCS on a scope would give some clues.
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