"Are you absolutely sure your encoders are counting correctly?  Have you 
turned each motor as exactly one turn as possible and observed the difference in
reading?  (This should be done in both directions with the pos option of the
diagnostic program.  Note the program starts with an oddball value of 517
in the position counters.)"

I tried this but as soon I run POS the numbers start scrolling on the page, is 
this correct? it will even do it when the encoders are disconnected.
See a screen shot here:https://sites.google.com/site/bmklawt/home/emc2/pos
Also did a com test: https://sites.google.com/site/bmklawt/home/emc2/commtest

The fact that the numbers keep going up at vast rates between axes
indicates something is quite wrong.  Are you absolutely sure these
values are being sent to the input scale parameter of the ppmc driver?
Possibly there is something wrong in your ini files (it would likely be
either in the .ini file or in ppmc_motion.hal, which reads the parameters
in the .ini file and sets the, into the driver with a line like :
setp ppmc.0.encoder.00.scale [AXIS_0]INPUT_SCALE

I believe these to be correct, you can see my config files here:
https://sites.google.com/site/bmklawt/home/emc2

If this line is somehow being tricked into picking up the wrong value
from the .ini file, that might be the problem.  You should examine
the actual value with the "show hal configuration" utility that is
available from the Machine drop-down menu in Axis.
Examine the values of  ppmc.0.encoder.02.scale, for instance,
and see if it is what you are putting into the .ini file.

I don't know how to do this


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