The license was a red herring, I was actually doing a different sequence after I removed the file which made me think it was the file causing the problems. (OK Mark McGrath no smart comments about consistency 

  )
Heres what I think now and I have repeated this quite a few times on different computers.
Test 1 
Open Mach 
Reference
Go to Zeros
Load G-Code
Move axis and zero
Close Mach and all is well as I get asked whether I want to save or not. 
Test 2
Open Mach 
Reference
Go to Zeros
Load G-Code
Move axis and zero
Regenerate toolpath
Close Mach and I DON'T get asked whether I want to save the new fixture. 
Test 3
Open Mach 
Reference
Go to Zeros
Load G-Code
Move axis and zero
Shift display mode 
Close Mach and I DON'T get asked whether I want to save the new fixture 
So looks like maybe there is a bug in the display mode and regenerate toolpath options.
 I would appreciate if a few people that have the latest version (or 1.90.035 onwards) could test this out. 
Hood