The most common cause for this is a spark plug that has accumulated a bit of extra lead or soot around the electrode. The engine generally will run fine in the Both position or on the other mag. One procedure that may solve the problem is to run the engine up to 200-300 rpm over normal run-up power with the ignition switch in the Both position. Then gradually lean the mixture to raise the temperature in the bad cylinder. Lean to the point where the engine begins to misfire, then richen slightly so it runs smoothly. The other spark plug in that cylinder will continue to fire and the combustion it ignites may burn off whatever deposits are on the electrode of the "bad" plug.
After running up for about 30 seconds or so, bring the power back down to normal runup rpm and go though another mag check. If the engine runs smoothly on each mag, you have solved the problem and can go flying.
In my case, this procedure didn't work although I tried three times. We taxied back to the FBO and the mechanic was called out (it was Sunday morning, of course). It was my fervent hope that the problem would not clear and my reputation would remain intact.
When he tested the mag, the engine still ran rough so that meant four possibilities: a bad plug, a bad ignition lead, a bad ignition switch, or bad magneto. The last three would have meant a big delay. Luckily, there was a small bit of lead shorting out the electrode of the top plug in the number one cylinder. It was almost invisible-about the size of a hangnail. A quick blast with glass beads in the plug-cleaning machine put us back in operation in 10 minutes.
Why check the ignition system every time, even though the engine was running fine just a day or even minutes before? Because, as this experience shows, problems can de-velop without the pilot knowing, especially when there is a backup system that will mask trouble.
Bruce Landsberg is executive director of the AOPA Air Safety Foundation.