EPCS16 AS Can't Verify Device (General AS Programming Issues)

I didn't notice from your previous posts, that you apparently are using a AS to multiple FPGA configuration scheme. I wonder what's the exact circuit your using in this case, cause I didn't find an Altera circuit example with multiple FPGA and AS programming interface.

It is necessary to connect the nCE pin of first FPGA to the programming connector as in the single FPGA circuit, otherwise any of the connected FPGA could drive out DCLK or DATA line, conflicting with the programming adapter.

If the circuit as such is correct, it could be a problem of, as you said, fairly long lines, but I didn't use multiple FPGA AS configuration yet and don't have experiences on my own regarding this matter.