Two kinds of EP4SE530H35I3N

I have two kinds of EP4SE530H35I3N chips. The packages of the chips are different, one is 1152 FBGA option 1 , and another is option 2, according to the package file of pkgds.pdf from Altera.

Both the chips are soldered on same board.

My problem is:

When download programs using JTAG, optiop 2 chip is good. While the option 1 chip stops at 96%. The error message is 'Config_down will fail to go HIGH'.

I am sure that the boards are good. I have used the chip of option 2 package for many times and never have any problems. This is the first time I use chip of option 1 package. So I wander what the problem is. Are there any different between the two chips? How can I program the option 1 chips (maybe using 0.95V core voltage as ES chips)?