Downloading on the custom MAX10 board with USB Blaster

You need to check a number of things - again probably. As you suspect, the Auto-Detect should work just as it does on your Cyclone IV board.

Is the MAX 10 device powered properly? Does every power pin have power?

Is JTAGEN pulled up?

Is nCONFIG pulled up?

Use a development board as a reference design and compare your schematic to that. Look at the documentation and schematic for the max 10 fpga evaluation kit (https://www.altera.com/products/boards_and_kits/dev-kits/altera/kit-max-10-evaluation.html), as well as the "max 10 fpga development kit (https://www.altera.com/products/boards_and_kits/dev-kits/altera/max-10-fpga-development-kit.html)" which uses the same device you're using.

Cheers,

Alex