jtag pin voltage levels

I understand that you are using a scheme according to Figure 8–28. combining jtag and as configuration schemes and have VCCIO for all banks?

Fig. 8-28 suggests 2.5V for the JTAG connector Pin 4 supply.

For the EPCS interface, I used to read a VCCIO suggestion of 3.3V for the respective bank from device manuals and support information. But it's not explicitely stated in the Cyclone IV device manual.