Very unstable JTAG chain on PCI Express Development Kit, Stratix II GX Edition

We have such board: "PCI Express Development Kit, Stratix II GX Edition",

http://www.altera.com/products/devkits/altera/kit-pciexpress_s2gx.html

It contains EP2SGX90 and EPM570 devices on the same JTAG chain. They are also claimed as multi-voltage.

Programming is very unstable (by Quartus programmer). Sometimes it detects two devices, sometimes it even program both, but often says "Error: Can't access JTAG chain", sometimes also "Error: CONF_DONE pin failed to go high in device 2".

Nios II IDE also cannot load anything inside Nios II CPU.

Is this JTAG unstability is connected somehow with multi-voltage feature?

USB Blaster is used, BTW.

Is there any special DIP configuration need to be set?