Heres a quick sketch showing what I am meaning as often its easier to put in pictures rather than words.
I think this is how your router is positioned when at home, so if for example the travel was X 800 and Y 400 this is how you would set up soft limits so that the machine coords follow convention. This may or may not have a bearing on your issue but its certainly worth trying.
Hood

Nice picture and I under stand now what you are saying,
I will give it a try in the morning FIY not a router but 46 x 60 x 32 vertical Mill we run large steel parts with lots of profiling and drilled and taped holes, I also have a HASS VF3 mill, do al ot of prototype work, To bad they both don't program the same, close but??
Thanks agin also  Mike

Hopefully it will help.
Sounds like a nice machine, post a few pics if you can
Hood

Hood
I have reconfigured the Y axis to home + and changed the soft limits accordingly, this also makes it easier to do a tool change and now I can run code G91 G28 Z0 Y0 and every thing goes where it should, if I steel have issues with x I will also change it will see
I have also change some of the G Code structure to see if there is any difference.
I hate trouble shooting intermenttent problems

Personally I would configure the X correctly as well, possibly wont help but could well be screwing with the offsets.
Hood

Hood
I have not reconfigured X requires hard wire changes
Every thing work fine without tool changes
tool path, DRO'S and all other displays are correct with or without tool changes
The current program has tool changes, tool 1 ran fine
tool 2 did not
after tool change program called for Y to go + went - no soft limit warning moved to over travel limit
you can see what I am talking about in the screen shot

Here is the screen shot

Not sure why you would need to wire things differently if you already have the Home switch on the X at the positive end. Just set the X Min soft limits to Zero, X Max to the travel and the home off to the travel. Then when you home the machine coords will be set. If you press the machine coords button you would see that it reflects the positive value that the axis is at, and if you did a G0G53X0 it would move to the opposite end, ie your machine coords zero for X.

So it is only when you call a tool change? What do you have Mach set to for Toolchange on General Config?

Hood

Tool change is set to
Stop spindle wait for cycle start
We have to change to manually
I will change X in the morning just to see if it has any impact

Can you try changing to Ignore Tool Change and insert a M1 so it stops for you to change the tool.

Hood