There is no scope inside the FPGA for it to 'short' these supplies together. Or indeed pull banks 5 & 6 to 3.3V via the other bank supplies.
You either have a design fault or a build fault. The fact you've changed the FPGA and changed the symptom suggests you had a build fault - I'd be guessing as to what that was without more detail.
However, given the 2.5V rail is still showing 3.3V I suggest you still have a design fault or a further build fault.
Did you, by chance, power the board when the FPGA was removed? Is your 2.5V supply giving out 2.5V - or 3.3V?
The schematic you've posted isn't readable (a common problem with images posted here). Perhaps try and post it again.
Cheers,
Alex