Is the error the same on all axes? Are the encoders the modular bearing-less type? If so, the accuracy would depend on the installation accuracy. If a modular encoder is not well aligned you could easily get 40 counts error over a one nominal 4000 counts revolution.

Dan

The signals go to a board that isolates the PC's parallel port

Might be something to do with the isolation although I would expect that to miss pulses if it was a problem rather than add.
Dan may be on to something, is it a bearing-less type of encoder?
Hood

The encoders always show more distance than the DROs, so there are no missing pulses but extra ones.

Some of you may have read my recent post about electric noise affecting my probe. The solution was to a dd a few small capacitors across the inputs.

I'm starting to thing there may be noise here too, although what's strange is that the results are too similar over repetitions. If the problem were noise it should be random.

Right now I'm using the same parallel port (LPT1) to control the 3 axis and also to input 5 of the 6 signals from the 3 encoders.

So in all the tests I've run every signal when in and out through the same port.

Would it make any difference if I use the second LPT port to input the encoder signals?
could this help get both the encoders and the DROs read the same values?

It may make a difference connecting direct to a port rather than going through a breakout board.
What about Dans question, what kind of encoders do you have?
Hood

Not completely sure although in the encoders data sheet ((http://gap-sa.com.ar/pdf/HE.pdf) there's a 'bearing life' parameter, so I guess the do have bearings. 

Yes they have bearings, the type Dan is talking about you place the encoder disc onto the motor shaft and the base fits to the motor and there are no bearings in it.
Hood

No, this is a completely separate unit coupled to the motor shaft with a plastic coupler to adjust miisalignments.

Now, any ideas why the encoders are not giving the same measurement as the DROs ?

This is driving me nuts. If I can't get this solved, I won't be able to use the machine in manual mode.