Mostly when I run EMIF debug toolkit, the "Link project to device" option autodetect 10AS066H1|10AS066H2, as you can see in the following picture, but the actual device in the JTAG chain is 10AS066N3F40.
That results in an error occurs when program the device in EMIF debug toolkit, a mismatch of hash.
Futhermore, even if when I run stp file, the result of autodetect is also 10AS066H1|10AS066H2, and the programming in stp file is much slower than programmer.
Also can try to reduce the JTAG frequency:
and what QII version that you are using? Probably can try with other version.