Pull up & pull down resistots on MSEL pins in Cyclone-IV E

There are some inconsistencies between Altera's documentation and a number of their own (and partner) development kits.

If you know which configuration scheme you are going to use I recommend connecting the MSEL pins directly to GND or VCCA. Remember, you will always have configuration via JTAG available, regardless of the hard wired configuration scheme you chose.

If you do need options (to chose between different configuration schemes) I suggest using 0R resistors.

Finally, many people (including myself) have had success driving the MSEL pins from a microcontroller or similar. Providing the MSEL pins are stable at the point at which they are sampled (ensure they are stable when you release nCONFIG), you are unlikely to see any problems.