I've run into this issue a couple of times where the Gate Agent will clear the non-revs significantly before the policy stated time of 30 minutes. The agent then fails to look prior to closing out the flight to see if anyone has checked in since they cleared non-revs. They seem to have the idea that non-revs have nothing better to do with their lives and need to be at the gate and checked in 60+ minutes from departure.

The best recourse you have is to submit a non-safety FCR, and check the box that requires a response from someone. I have done this twice with positive results (including a straight out apology). Granted, it doesn't help you at the exact time of travel, but hopefully it leads to a change at the gate agent level (policy, procedure, memo, etc.)

I also use the technique of checking in online. To me, it eliminates the stress of not being cleared. But even that is not fail-safe. Depending on the city, online check-in runs the risk of the gate agent using the old-style of calling each non-rev to the podium and assigning seats when they show up. But, that method seems to be becoming more and more rare.