I struggled with specifying the clearances the way Electra requires them in the “.DO” file only to find that it didn’t seem to use them. I recalled that in the “.DSN” that is created when you run the PCB_to_DSN.ulp from Eagle, there is a set of clearances specifications defined according to the Net Class clearance matrix.
Well, it turns out that in Electra, these Class rules always override the PCB rules in your .DO, so the latter are useless.
A quick fix is to set all your clearances in Eagle’s Net Class matrix to 0 and always use the .DO to specify your clearances.
This is Eagle 5.11 & Electra 2.9.3.