The meaning of these two terms depends on the programmable logic device (PLD) used. Lattice provides three kinds of technologies in the PLD products you purchase. The technologies are:
For the EEPROM based devices the two terms are interchangeable. For the other two technologies there is a distinction between the two terms. Programming refers to the process of erasing and reprogramming the non-volatile memory used to store the devices bitsteam. Configuration refers to the time period the PLD is retrieving the bitstream from the non-volatile memory. The data retrieved is loaded into the PLD's SRAM, which causes the PLD to take on function you have designed it to perform.