It is marginally possible that the table is not flat. It is more likely that the ways are not machined true to the table top. It is possible that something is bent or bowed. It could be a tolerance issue in the gibs that allow the table to sag in certain areas of its stroke. Indicating in this manner only shows what is happening at a single point as that point is riding through the ways.
However machining the table top may improve things (until you make adjustments to the machine again).
Won't hurt anything to give it a go.