Can I assume that, with the switching regulators, VCCINT & VCCIO look OK at the FPGA? Is there suitable decoupling locally such that the switching noise the FPGA is exposed to is minimised?
I feel this is more likely to be conducted heat rather than heat generated by the FPGA. Do any of the LT3690 power circuits generate much/any heat of their own? How close are they to the FPGA? Are there any other circuits on the board dissipating heat?
By bypassing them, and powering from the bench supply, your target is not going to generate as much heat - heat which could be conducted to your FPGA. The temperature of the device is dependent on both what it is doing and the heat generated around it.
The Altera Power estimator is only going to consider power the FPGA generates and will assume no other heating sources around the device.
+9 degrees doesn't seem particularly bad to me. What delta do you see at the FPGA if you leave the board powered but don't configure the FPGA? Do you get this same behaviour on multiple boards (assuming you have more than one)?
Cheers,
Alex