--- Quote Start ---
Stupid question: you've selected the .sof file generated by Quartus as the file to use to program the board?
There also may be error messages indicating why the programming failed. You might have scroll the Messages window a little in the main Quartus window to see them.
--- Quote End ---
Yes, I selected the .sof file and checked the "Program/Configure" box.
I just created a new project, just two inputs to an AND gate, one output, pins correspond to switches and LED. Still fails to program.
The messages I get are:
https://alteraforum.com/forum/attachment.php?attachmentid=13927&stc=1