Eagle EDA does have an unattractive feature. Running the CAM process produces results that has a random X,Y offset added to the real numbers.
Here is my workaround:
Make sure your entire design is located +X and +Y (above and to the right of) the little '+' fiducial on your screen.
In your source file, place a 0.001" hole at some obvious location on your board near the lower left corner. I shall use X 1.0, Y 1.0 for example.
Run the CAM process to generate your Excellon drill file. Remember to manually add the '.txt' suffix to your suggested file name for results and remember to click on the dialog box *twice* because you are processing both 'pads and vias' and 'holes'.
Open your Excellon *.txt file and find your 0.001" dia hole within. Note it's location.
Run the CAM process once more and edit the 'offset' variable to cancel the offset in the results file. Recently, for example, I cancelled their error when I plugged in an offset of X = 0.0010", Y = -0.0151". The 'Y' offset will eventually show up as a metric value while the 'X' offset will remain in olde englishe inches. It's a feature. :)
Run the CAM process again and confirm that your 0.001" hole is now shown at X = 1.0000, Y = 1.0000 in the Excellon file.
After every few edits, run the CAM process again and adjust your offset as necessary to bring your 0.001" hole error back to zero. Make note of the location of a nearby 'real' pad or hole for future reference.
Just prior to generating your real CAM files, delete your
0.001" hole and use the location of your 'real' pad or hole as a sanity check for your real CAM output.
--Winston