my guess is a loose connection, bad pins in harness, or cold solder joints. my suggestion is to pull panel apart and wiggle the wires around the harness area while you have a friend press the switches. also check to see if there are any loose connections or bent prongs in the harness. check all fuses in vehicle. also, if the connections where made via solder, cut joint off and resolder every connection around your problem area.

if all else fails...remove your keyless entry system and put everything back to stock and test.

otherwise time to take a trip to the shop.