Eagle - Router does not understand wire jumpers?
It wouldn't. You've told it that the net must be connected, but it has no way of knowing that your jumper wire is a connection. Anything in your schematic that you connect up must be connected with copper on the PCB.

For jumpers what I do is add an extra copper layer. If it's a one layer board, make eagle use two layers. Then connect the two sides of your jumper directly together on the new layer (do not place anything else on this layer).

For manufacturing, you simply don't generate Gerber data for the extra layer. So after manufacturing there will be no copper there and you can instead install your jumper.