Eagle is really powerful - it has a LOT of features that aren't used by the hobbiest but are there for serious manufacturers.
Not sure what you mean by dotted traces.
I'm not sure that two versions would be useful - the extra traces would be bad too for those of us who are stuck etching (very jealous of your milling abilities byt he way)
As PaulS suggests, these extra traces are most probably on another layer besides the top and bottom layers - by default 1 and 16.
Before I make a printout of the finished board for etching I turn off all layers except the top, bottom, dimension, pads and via layers.
Maybe post a screenshot of these extra dotted traces?