It sounds like you are doing the RFH with a tool in the spindle, somewhere in the program after the tool change operation. Perhaps I am mistaken, but RFH has never given me a problem, but follow a basic convention in all my programs as follows.
1. Before all M6 T## H## commands, I put a G53 Z-.05 line in.
This moves the spindle to it's highest point, .05 inch below the Machine 0, before the tool change cycle.
This is exactly what Hood is suggesting you do; in fact I learned this method from him in another post some time back.
2. The line after the G53, and before the M6 line, I add; G0 X## Y##, position that moves the spindle closer to the front, away from the work surface.
This moves the spindle out where my longest tool is easily put into the spindle, which might have been too close to the work before.
3. I preface the G53 line with a (Tool 6 - Boring Head) or some such tool name in parentheses , so when I scroll down to do the RFH line I can easily find the
place I want to go.
4. This "name line" is the program line I use for RFH.
Doing the RFH
Remove the tool from the spindle.
Scroll to the name of the tool, highlighted.
Click on RFH
Do all the OK's for preparation move.
Machine goes to tool change position, and calls for tool change.
When proper tool is in spindle, hit Cycle Start. Spindle starts, spindle moves back to the work, and program starts where you want.
This is assuming you have run the whole program before without tools, and with tools, proving there are no "gotcha's" ready to crash you tool.
Mach3 has some various little problems, but RFH is not one of them. I find having all my tool changes (for a knee mill) with this kind of additional
stuff, like the G53 moving the spindle way up, and moving away from the work to be a simple, and safe way to proceed through a program.
Just because you think the RFH should have all the right numbers in it's memory, at any given point in the program, it may not.
A lot of things Mach3 does are not documented, or totally sensible to our way of looking at things. It is an elaborate machine program, that has evolved over the years. With a conservative, cautious approach, Mach3 is a superb, amazing machining program that can be depended upon.
John