Just another thought. Had a chat with some people re the pop up and cancelled plans. When a flight plan is filed, the activation pre your boundary may be according to the times quoted on the original plan. If the aircraft is late, it may be outside the parameter where the system expects the track to be activated. Therefore it may automatically cancel the plan. You need to take note of a couple of these plans that do not appear, get the original with the times at your boundary and see if a pattern emerges. Re the real pop ups, I agree, you cannot mess about with other peoples safety, however maybe a bit of pilot education would be useful, preferably over a beer at a local controller/pilot forum. Even if it only reduces the problem, it may be worth it.
Sorry not to be more precise about your disappearing plans, but at a distance it is difficult to accurately identify the possible alternative answers.
To others on the electronic strip forum, this shows how wonderfully flexible the old paper strips were, BUT, entering data on an electronic strip/data line does give information to all interested parties, after all, that written on a paper strip is known only to the writer at that moment. We are probably not 100% there yet, but with fora like these, it certainly helps to identify the problems.