Hi Bruce. Maybe I'm not doing the EEPROM commands. I think that's what I'm trying to set up with Roxy's directions on page 8 and my questions above. I suspect that that might be the culprit. Until I hear back from Roxy I'll go ahead and find those EEPROM commands and issue them.

For my normal workflow, what I do is I open my configuration.h file and then go to my printer and to a G29 and then a G28. That 'homes' everything and does an Autolevel. When the autolevel stops, my hotend is sitting there with the probe 'up' waiting to start a print. It should be at the perfect offset distance. I issue a G1 Z0 and the hot end will move down to the bed. If all is good with my configuration.h file, then the head will stop and I'll have that "sheet of paper gap." If it's a hair tight, I go to my configuration.h file and add 1/10th mm to it, do G29 and G28 Z0 again. Most of the time that's it. I close Arduino and I should be good to go. That's I do though. I haven't been issuing and EEPROM commands after the G1 Z0.

So continuing my standard workflow that I just mentioned, I now go to print with say Slic3r, and it's about 2mm high off of the bed. So, I switch to any other slicer, and they too will be off but not the same amount. So, I'm constantly now refining each slicer and it's just gotten way too tedious considering I have autoleveling going.

I think what you are suggesting is that I'm missing a step. Are you saying that I need to issue some EEPROM commands after I flash the RAMPS? I need to find those, I think they are in the 500's if I remember earlier comments in this thread. Let me try that and report back.