Hi Neil
I believe the Eagle light version will not route outside the square defined by the diagonal points (0,0) and (50,50), metric. You will be able to load larger boards with more layers, created by the ‘standard’ or ‘professional’ versions, but not to work on them much. You can probably draw tracks outside the 50mm square using the WIRE command or button, but not ROUTE. I suspect it may be possible therefore to generate a larger PCB than 50 x 50mm, but only as a completely manual exercise, without the schematic integration and design rule checking that the program offers.
You also cannot ROUTE over an object in the Dimension layer 20, on any tracking layer. You could WIRE over an object and then connect this track to the relevant net by using the NAME function. A DRC will then show an error, but this may not matter? Similarly, you cannot ROUTE over an object in the restriction layers 41 tRestrict and 42 bRestrict, for top or bottom side tracking respectively.
On the schematic, I take it that all the wires are correctly drawn on the Nets layer 91, and not drawn on another layer, in which case they would not be electrical connections! If you MOVE the component on the schematic, you should see all the wiring ‘rubber-band’ and stay connected to the component.
There is a helpful message board system on the CadSoft website which you could try. I have found CadSoft to be responsive to technical queries, but possibly only on the registered (not ‘Light’) versions of the product.
Hope this helps
Martin
(Occasional user of EAGLE, which I prefer over other PCB design programs I have tried)