I recently had a board (just this week) where I had 3.3V hooked up to VCC pin on the JTAG header for a PCB. The JTAG header was for programming the EP3C5 part and EPCS16 through indirect jtag configuration. The 3.3V on the VCC pin of the JTAG header was a mistake in the schematic that propagated to the PCB. However, since the board had controlled impedance & stackup, I thought I would go ahead and try to make the board work. The FPGA programmed about 3 times, then after that, it quit. I could recognize the FPGA through the JTAG pins in the Quartus programmer, but could not program it. I've put 2.5V on all JTAG VCC header pins before this, and indeed this PCB issue confirms that 2.5 is essential. I know that you can use clamping diodes if you use 3.3V, but this seems to be extra components when simply using 2.5V will work. I am curious if anyone has consistently designed the JTAG header at VCC of 3.3V and had the FPGA successfully program time after time? With or without clamping diodes?