With my Mach3 driven lathe, I am still a bit in the dark about limit references. On power up, I set the limits on both axis, but my limits switches aren't perfect, and I get the odd change, nothing bad though, maybe .005". I haven't figured out yet if there is a way to power up the machine, set the limits, and have it not change any of the reference settings. With a lathe, with indexable tooling, you can pretty much set your tools, and never change the tool offsets again, save for wear or the odd mishap. If I power down the machine, I have no reason to manually move the saddle or crosslide, and make it a practice not to, so when it is powered up the next time it would make sense for the control to just store the last position and go with that. I agree that you still should set limits in case the saddle, etc. has been moved while the control was off somehow, but the limits setting procedure should not alter the machine's absolute position. This then nulifys the inaccuracies of the limit switches.