IMO the intruder entered the apartment via the front door after Matthew had made his way back to the Tapas following the 9pm check. Having been in the process of sedating Madeleine in the children's room, he/she was interrupted by the unanticipated sound of Gerry opening the patio door (a door noisy enough to be heard in the apartment upstairs).
There were only 2 places the intruder could have moved to quickly without being seen by Gerry - the bathroom or the parents' bedroom. Bathrooms generally have few hiding places (Psycho-style shower curtains aside) so my assertion is that he/she entered the parents' bedroom & hid behind the floor-length curtains at the window. The PJ did not forensically test the parents' bedroom on 3/5/07 or thereafter for prints/hairs/footprints/DNA.
That scenario accounts for 2 door moves before the 9.30 check.
All MOO.
I like your reasoning misty, but how could the abductor have got across to the parents bedroom without Gerry seeing him? It doesn't take long to open a patio door and step in.
Also, i am doubtful if the abductor could have even made it to the bathroom in the time to open that Patio door and step in
Unless, of course, he was last minute warned by someone outside watching and just had the time to do that before the patio door opened. All very risky though.... and he must have moved on from the bathroom because Gerry used the loo before returning to the restaurant, didn't he?