Bad cable. Cables goes bad and if you don't test your cables on a regular basis, then the issue will most likely show up during a line check. A product like the Ebtech Swizz Army cable tester can tell you when a cable has gone bad and the issue with the cable. Keep spare cables of all types because you will need them. On a related note, having the right tools like a line tester helps a lot. Check out this list of tools for your gear bag.
Bad connection. Plugs aren't always pushed all the way. Typically I see this with guitar cables into the guitars or cables into guitar pedals and di boxes. A simple reseating of the plug should resolve the problem. This goes for all cable connections including XLR, TR, and TRS.
Dead batteries. These might be in an effects box or, where i usually see it, in the onboard EQ/Amp in an acoustic guitar. Keeping a few 9V batteries in the booth comes in handy in these situations.
Wrong wiring. Plug A into B, not C. Following the signal from the source to the mixer, you should be able to find where the wires are plugged into the wrong place. Typically, an input is plugged into an output. We, in the sound booth, see everything coming INTO the sound booth. Musicians, on the other hand, see wires coming TO the stage. Fix the wiring and then educate the musicians if they do any of their own setup.
Poor microphone location. While you might see a signal, if it's not in the right location, you might not get enough signal for proper gain structure. You might not even get a signal because the microphone is too far away. I can see this point as more of a sound-check issue but I say the sooner you can resolve it, the better.
Broken equipment. Be it an active di box, or a broken microphone, equipment will break and you have to be ready for it. Keeping extra equipment around does pay off. Replace any equipment that is "just hanging in” before it breaks. If it works "most of the time" then it's unreliable and needs replacing. You don't want to spend your time mending equipment each week when it could be better spent on the sound check.
Channel labeled wrong. Of course there's no signal, nothing is in that channel! Sometimes mistakes are own fault. Just fix it and then ask the person on stage to try again. If they ask what was wrong, just say it was a board problem. :)
No signal from guitarist/bassist. This happens when they turn down their volume pedal, have their setup set for tuning, or have done something else to disable their rig from sending a signal. Ask them to check their volume pedal and any effects board options like being set to tune or mute. The increase in use of digital effects pedals in the church environment means an increase in the likelihood of this issue occurring.
Pastor wants to add a video. Hey, this stuff can fly in at any time. I'm just sayin'.
Bad mixer channel. This is the most frustrating because it will result in money and probably require a substitute mixing board for a while. When it does happen, try another channel and mark the channel as bad. Definitely escalate this issue up the chain o' command ASAP.
I remember freaking out when I couldn't get a signal from the stage. I thought there were so many possible problems and I had no idea where to start. It's great being on the other side of that and knowing it's usually a simple solution. And I think that's how most audio problems should be seen.
The solutions to most line check problems aren't complex. However, knowing what can go wrong, you can now provide solutions much faster. Line check problems aren't the end of the world so don't treat them that way. Knowing what to expect, you can view these problems as speed bumps.
Question: What Problems Have You Found During a Line Check?
Twenty five simple yes/no questions so you can score your last time behind the mixer. I could easily come up with another 75 but these cover the basics. A scorecard is a great way to establish a baseline for where you are and where you can improve. Up for the challenge?