How come every time a flight is nearly full my checked-in listing suddenly disappears because per gate agent "I must have forgot to "ACTIVATE" it"?

It's really frustrating to check-in for the flight home with one standby and a few airport standby, then fly all day, get to the gate ready to go home and discover you are no longer on standby and 30 folks "checked-in" in front of you...

I'm not complaining about the rules, I'm not happy about the rules being implemented incorrectly or not followed. Yes, I'm watching it closely and I'll be submitting documentation. The sad part is management will consider it an isolated incident while I believe it is more systemic.

Of course, airlines can make you paranoid, so, anybody else noticing this?