Recently, optically reconfigurable gate arrays (OR-GAs), which consist of a gate array VLSI, a holographic memory, and a laser array, have been developed to achieve a huge virtual gate count that is much larger than those of currently available VLSIs. However, comparison of conventional ORGAs with current field programmable gate arrays (FPGAs) reveals one important shortcoming: they are not reprogrammable after fabrication. To remove that shortcoming, a programmable ORGA (PORGA) has been proposed. However, a PORGA must implement a window to detect holographic memory patterns. A PORGA window might have scratches, fingerprints, or other defects that could occur while a PORGA is used. Even under such situations, a PORGA must be programmable. This paper therefore presents influence analysis of a holographic memory window of a PORGA. It has been demonstrated that even if a window of PORGA has scratches, fingerprint, or defects, a programming procedure can be executed correctly.