Config Done Fails to Go high with simple SOF file(Jtag+USB Blaster)

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We are using the Combined Jtage/AS config setup

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The reported situation isn't completely clear to me. You should tell, what's the exact hardware configuration, e.g. referring to an Altera schematic.

In some situations, it's necessary to deactivate the on-chip configuration controller to assure, that the JTAG configuration isn't disturbed by tries to load an AS configuration. It's a Quartus Programmer option, that should be selected.

If basic JTAG configuration still fails (config done fail), it's most likely a hardware problem.