Just a tidbit for anyone else who runs into this problem. To change EAGLE 4.16r2 to use a 2.3 leading zero drill format modify the following sections of the eagle.def file in your installation of eagle. The eagle.def file is located in the bin directory of your eagle installation. Relevant changes are shown highlighted in red.
[EXCELLON]
Type = DrillStation
Long = "Excellon drill station"
Init = "%%\nM48\nM72\n"
Reset = "M30\n"
ResX = 1000
ResY = 1000
;Rack = ""
DrillSize = "%sC%0.4f\n" ; (Tool code, tool size)
AutoDrill = "T%02d" ; (Tool number)
FirstDrill = 1
BeginData = "%%\n"
Units = Inch
Select = "%s\n" ; (Drill code)
Drill = "X%05.0fY%05.0f\n" ; (x, y)
Info = "Drill File Info:\n"\
"\n"\
" Data Mode : Absolute\n"\
" Units : 1/1000 Inch\n"\
"\n"
Just Why does 2.3 leading zero even matter? I'm not sure it really even does anymore. Many years ago when batchpcb and golden phoenix PCB first hit the scene they were pretty stringent on the drill file being a specific format. I think the process of submitting PCBs has advanced far enough now that nobody may even care how screwed up the drill file is, but since I have always had good success sending it in the required 2.3 leading zero format, i figure why change a good thing. I did recently send some boards to SeeedStudio in a quite messed up drill format and they processed it just fine so maybe nobody really does care anymore.