Background: 
I am using a Tormach PCNC 1100
Need to make a small run of parts, but dont have a tool changer.  In order to save time I purchased a second vise.  My intention is put one part in each vise, and it would machine the first tool on both parts then pause and ask for tool 2, repeat operations for the second tool on both pieces and repeat.  there are 3 total tools necessary.
I had Solidcam generate the Gcode and I edited and spliced it all together and added the offset information.
I installed both Vises, put work peices into both, and Zerod them using a touch probe for G54 and G55 offsets.

PROBLEM:
The first operation uses a 3/16 endmill to create a pocket (through hole).  The G54 code worked perfectly.  The machine switched over to the G55 code.  My code is set to plunge to a clearance height of .020 and then start helical plunge.  Before the Tool reached the .020 depth is was already in contact with the work piece.  The crash was mild im guessing it hit the piece at around .025 and since the pocket is a through hole there was no major damage (luckily).  The job continued.  The second tool is a 1/8" endmill that just does a finish pass around the walls of the pocket.  I assume this worked correctly and to the correct depth but since its a through hole I can not confirm this now.  Finally the last operation is a Chamfer Mill around the endges of the pocket.  Both parts come out with an identical chamfer  (I think if the tool plunged an additional .020 on a chamfer it would be VERY obvious)

PLEASE HELP

Other notes
The parts are identical but the vices are not so the Z offset each work offset is different.
X and Y coordinates for both work peices are accurate
I have checked the tool length about a dozen times
I have restarted my PC
Rehomed machine and rezero'd both work peices

%
(05-MAY-2014)
G90 G17
M9
M5
G00 G40 G54
G0 X0 Y0 Z6
(TOOL -25- MILL DIA 0.1875 R0. MM )
M6 T25 G43 H25
G0 Z2
G0 X2.0895 Y-0.3652 Z2.
M8
M3 S3659
(--------------------)
(P-CONTOUR15 - POCKET)
(--------------------)
X2.089 Y-0.365 Z0.75
Z0.02
G3 X2.089 Y-0.365 Z-0.003 I0.0308 J-0.0294 F4

SEVERAL LINES OF COORDINATE CODE

G0 Z0.75
M9
M5


(-----------------------------)
(START G55 For the 3/16 ENDMILL)
(-----------------------------)

G00 G40 G55
G0 X0 Y0 Z6
(TOOL -25- MILL DIA 0.1875 R0. MM )
(M6 T25 G43 H25)
G0 Z2
G0 X2.0895 Y-0.3652 Z2.
M8
M3 S3659
(--------------------)
(P-CONTOUR15 - POCKET)
(--------------------)
X2.089 Y-0.365 Z0.75
Z0.02

THIS IS WHERE THE TOOL CRASHES AS IT RAPIDS DOWN IN Z

What is the height difference between the vises, and what are your G54 and G55 Z offsets?

Since I am sure someone will ask about if my offsets are correct