Which way SHOULD it be done? Programming both the FPGA AND the flash? Why would that even matter? I don't download anything to the FPGA when I use the command line, and that works.
The way I understand it, when you program the JIC file, the programmer downloads a flash loader to the FPGA which handles the interface to the flash. Here's a screen shot.
When you include programming both FPGA and flash then it will start to load Flash Loader into FPGA before programming the flash. without this you will observed that the Flash loader IP is not loaded.
May I know if you are able to reduce the TCK clock frequency to 6Mhz? May I know which Quartus version are you using?
You are using USB-Blaster II and not ByeBlaster. Please refer to https://www.intel.com/content/www/us/en/programmable/support/support-resources/knowledge-base/solutions/rd06242013_922.html on how to change the TCK frequency.