Unless you are mixing units and programming the wizard in mm on a machine setup in inches it is simply not possible for the wizard to make a longer move. The wizard simply writes gcode. Use the MDI bar and enter a move, like G1 z1 and see if Z moves exactly 1 inch.
First look at the setting in the general config- do you have it set for automatic tool change? Then look at the M6 macros in your macro folder under your profile name. Also it looks like you entered on 1 in the tool number- for turn operations the tool number must be in the form of 0101 which is the tool number and the offset number to use. When you enter the number in the DRO it will only show as 101, VB likes to wipe off the leading zero.
I don't think thats a glitch. I believe the X icon is a direct window command and windows blows the program away without giving it a chance to clean up. Thats why apps have an Exit button. Behind it I can have code to do anything I need to do.