I guess I need to clarify my issue a bit.

I'm usually using multiple tools in a single program. I understand that I have to adjust the offset of the tool every time I change a tool out in the offset menu (my first attempts including rezero'ing the DRO's about a month ago for every tool. Obviously I learned that quickly). With how I have been using Mach 3 for about a month now I've gotten all of the basics figured out. When I initially start mach 3 up, I set all of my DRO's to zero where my zero point should be with the first tool I intend to use in the spindle. This way I am completely ready to cut when I load my gcode into mach 3. I then load the program into mach 3, regenerate toolpath and do a jog follow around my workpiece watching the mach 3 screen to make sure my cutting area is where my workpiece is and that I'm not going to cut through a hold down. After that, I click the start button and the program starts. It runs down the initial G code until it gets to the point where my first tool is 'entered' into the program (as a tool changer would need to see). Mach 3 halts the gcode, a yellow LED flashes signaling tool change. From there, I always just click cycle start and start my program because I already have the tool in.
I am running into issues if I used this particular tool in a previous program and set the offset up on it. For example, Tool 13 is the initial tool I am using and have setup everything for. My program runs and gets to the point where it wants me to put in tool 13. I click cycle start because its already in there and go about my business. BUT, I have been running into issues if I used tool 13 ever before in any program and set the tool offset on it. Mach 3 remembers this tool offset and it incorporates it right into the program ONLY after I've clicked cycle start to run the program again. I forget to make sure there is no tool offset entered and this has caused me issues several times. Its one of those redundancy things where I have to zero Z over and over and over again, so I tend to forget and skip this step.
I am wanting to know if its possible to keep mach 3 from remembering previously entered offsets for tools after I shut it down. As my machine is homemade and my tools are at different heights everytime I put each one in, they are never the same exactly. So, everytime I change a tool out I have to do the offset anyways. I just never expect that to apply to the first setup because I zero'd the tool already.
GER21- I've been looking at making an auto tool zero gauge block. I actually posted about it when I was still researching on here a few months back. I should have one made this week, but right now I am trying to prioritize and get some hard stops done so my gantry stays on the table when I'm stupid and get limit switches functioning. I designed up mounting blocks for the limit switches over a month ago, I just havent cut them yet.