TP, The error is usually close but not 100% exact all the times. I thought about trying to adjust the ppr setup. Right now is setup in 800 and using something like 803 doesn't sound like a proper way to solve it. Anyway, the error is not exactly the same all the times.
RUSS, I know what you say and I saw it when I ordered the encoders. The encoders are HE50B-8-1000-3-T-24, so based on the model # they are 1000 ppr and that's what I ordered. The only thing I missed when I ordered was to try 5v instead of 24v. Now I put a BC547 transistor on each signal to adjust form 24v to the 5v I need at the board input.
The board I'm using to interface with the LPT uses a 74HC244P to isolate the LPT from the machine, although I don't think this could be causing a problem.