I'm not sure what kind of screening happens to bags internally post checkin but I know from 30-40 of my own flights within Malaysia and KLIA outbound (internationally) that typically checked in luggage is pre-screened by MAHB upon entering the check in area. This is typically a larger carry on style scanning machine (rapidscan) and on exit the bags receive a sticker from MAHB indicating the bag has been scanned. Carry on luggage does not need to go through this scanning. Upon checking in the bag while getting a boarding pass the airline agent will look for this sticker and if not found will require the passenger to go get it scanned at the entrance again. Now if the checked in bags are not rescanned post-checkin then there are serious holes here as the stickers are easy to manipulate such that they could be transferred from one bag to another, or the scanned bag reopened and "resealed." Additionally it's not difficult to get an unscanned bag into the checkin area (although this varies by airport, but commonly just enter via the exit) and then transfer a sticker. The ticketing agents aren't exactly checking the stickers in detail either. However, all of this hinges on checked in bags not being rescanned yet another time before being loaded onto the plane. Based on the number of glaring holes apparent it would seem they most likely are scanned post-conveyor and the pre-screening gates are mostly superfluous/feel-good.
That being said, my gut feeling is some kind of catastrophic event in-flight and I'm not so sure how much I believe terrorism/bombing is behind it. I only throw out the bag details because one never knows these days.