Yup, as David said, you don't want to measure at the bearing as they have their own play in them. Here's the thing to remember when checking tools for runout, you want to eliminate as many sources as possible. So if you try to measure the runout of bearing on a bit in a router that's mounted in a table, you have so many potential sources of error it would never be reliable. If the router base is off to the table by a fraction of a degree your going to have runout, the bearing as mentioned has runout....too many places for it to add up. The only reliable way to check IMHO is to attach the dial indicator to the base of the router, insert a known straight piece of rod, and check the collet to the base.

Anyway it sounds like you have solved your problem for now, and learned a little something along the way

JeffD