If someone doesnt use a proper puller to remove the balancer, or worse yets hammers on it, that might cause a problem. I have heard of, but not personally seen, the outer section of a balancer slipping around the inner, causing the timing mark to be off.

But as PWD stated, your vibration is likely elsewhere. If it occurs at a cetain vehicle speed, then its definately in the drivetrain . If it occurs only at a certain engine RPM, then likely within the balance of the motor itself (and yes as he stated a dead cylinder would do it). Of the two, driveline problems are way more common.

If u-joints check out, a wheel or tire would be good place to look. Have someone follow you down the road in another vehicle, looking at all your wheels/tires. I have seen some real bouncers trucking down the hwy.