Hello Mike,
Thank you for your reply. Definitely the signals rise/fall time and levels are very important.
I have the micro-controller with pins outputs push/pull mode and the signals are shorter rise/fall time (approx. 10ns 10% to 90%), compared with USB Blaster used to program .pof file over the same JTAG interface.
The clock frequency I use is lower than used in Blaster, and the calculated delays when generating .svf file, should be longer than required.
I was able to generate a version of the .svf file doing only erase and verify the blank memory using the Blaster.
Thank you anyway,
Dan