There's a lot of reasons why an airplane may go "missing." It happened to me once a couple of flights ago. I was running the radios, and thought I had checked in, but when I called about something a few minutes after the frequency change, I found I had forgotten to check in. I got busy doing stuff.
Often, you may change from freq 1 to 2 to 3 to 4 in a VERY short period of time, and besides making it busy, you can remember just checking in 30 seconds ago, which was true, but you need to check in again.
Sometimes the controllers forget to transfer you, or sometimes they give you the wrong freq. This also happened to me recently. I went to the new freq, and no one was there, and by the time I went back, no one was there either. I had to look at frequencies on the chart and randomly try the center I was supposed to be on until I found one that worked.
Sometimes the pilot's are talking on multiple radios, and may have checked in on the wrong one without realizing it. Other times, when you check in, the controller is busy, and you get no response.
Other times, the freq congestion has been so bad I couldn't check in. Once, the controller assumed I was on (it was VERY busy) and just gave me instructions. When I answered, he knew I was on his frequency. On several other occasions, when the controller finally had time, he asked me if I was on, as he knew I hadn't had a chance to check in.
Over the Red Sea one time, we went lost comm for 20+ minutes (mostly because of a lack of radio coverage) and almost had a mid-air with a civilian 737. I'm assuming they had TCAS, because they were taking an evasive manuever when I first spotted him.
Using satellites to communicate and having a data-link will drastically cut down on these problems. I read somewhere that up to 40% of the voice-on-frequency time is used just to change airplanes to new frequencies.