Do you mean the keel bolts (not the rudder bolts)? The wells under the floorboards are above the keel. If you really mean the rudder bolts, that is, the bolts inside the transom that hold the rudder pintles, that would be the lazarette area or maybe one could call it the bilge, under the cockpit, that is filling.
You might have a bad keel to hull joint, or issues with the keel bolts. You may also have water seeping in from elsewhere. Can you see if the wells refill by water seeping in from the weephole, such as the one between the forward well and the v-berth area? When mine gets quite wet, enough to have water seep forward, it does weep out of the forward area and into the wells, and I have to keep sopping it up until all the water weeps back down. You could also have a bad hose under the anchor locker, which would let rainwater into the hull forward of the v-berth, which I suppose would seep under the v-berth and eventually to the wells. You could also have a bad deck fitting, such as a lifeline stanchion or chain plate cover.