I did try a search...
Smooth stepper with latest driver
look ahead I have tried 20 to 200 lines
Here is what I am seeing on 3 different machines with the latest .40 mach ver registered
Create a g code with the pocket wizard.
Zero out machine and dry run g code. 
press  FEED HOLD
Jog all axis`s to different location
Press the run from here button
Cycle start and I get the preparation move box

I notice that Y axis prep always has 0 in it.

on .020 with a printer port  I cannot run from here at all it puts me in the Cycle start / prep move/cycle start loop

Any ideas?

Screen shots

showing DRO`s  and Prep move
the forum is pitching a fit wwith uploading pics

they are out of order in the list but should go from
feed hold
jog move
prep move

Never had that issue with the SS so as you also have issues with the PP it may be a problem with your setup. If you attach your xml I will see if I can replicate it here.
Hood

im not worried about the PP machine, do you want the SS XML?

XML off off the SS box with the Y0 post. error

Ok will test it out later, just heading home in a few after I finish a job.
Hood

just for argument sake, I upgraded mach to the .053
Still no change

another test
mach 3 on my laptop...... bare install using the default xml  No plug ins of any kind.
vers .028

I still get the y0 on the prep move

Ok just run it here with roadrunner loaded and  then did a RFH and pressed start and prep move box had correct Y in it. Can you attach the code that you are using and also say what line you are starting the code from by RFH
Hood

I think I figured it out.
RFH does not like radius commands.
I used the circular pocket wizard with X and Y as the center.  So the code had y0 in front of every line.  Then a radius off of that.
Explains why when you RFH after jogging each axis, the prep move wants to go to Y0  which does not put the tool back into the same position as when the machine stopped.