Back in the late 80's it once took me 3.5 hours to clear passport contol at Newark, even though I was one of the first off the plane (I'd arrived SLF on a Virgin Atlantic 747, Upper Class, from LGW). When I cleared passport control the queues were still out of sight and into the corridor beyond the passport control area. I can only assume that there had been some kind of heightened state of alert or maybe the automatic passenger screening system was down and they were having to clear everyone manually.
Not long after 9/11 I returned from MCO as SLF. Check-in took an hour and a half because they had to request a manual security clearance for each passenger before issuing a boarding pass. We'd been forewarned of the delays so we were prepared for them.
These sorts of delays, albeit not too common, are one of the "pleasures" of international air travel.