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Hello,
I am getting the very same error message :
unexpected error in jtag server -- error code 45 when trying to program a non-volatile key (.ekp) into a Stratix II.
The JTAG chain is well detected.
The Ethernet Blaster II's firmware is up-to-date (April 2016).
No problem when programming the external flash (.jic)
Also, programming the .ekp with a former Ethernet Blaster (not II) works flawlessly !
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After I posted my original post I did find a solution. It a long time ago but from what I remember, it was due to incompatible programmer firmware & hardware combination. I think I had to reinstall the application as well.