Check my mechanical notes on the v3 build. This can also be the cause of many first layer leveling issues:
http://forum.seemecnc.com/viewtopic.php?f=112&t=11104
Let me first say you guys are great! We are and have been actively investigating this mhackney and miaviator! We want everything to work perfect! We've had very in-depth discussions all day and we have a few things to check in the firmware. Look for a ***possible*** firmware update by the end of the week. We will know tomorrow, which after thorough discussion, Oly will dig into it on the firmware side, we can not say there is a minor problem yet. This took hours of several of us testing and 'breaking' things on purpose (firmware, eeprom, and mechanical). So give us a moment.
I also want to apologize ahead of time if I missed something in your post. I'll be honest - I scanned quickly through this posting and just want to add some comments.
Keep in mind that an average human hair is roughly 0.003inch (.076mm) diameter. Let's keep in mind this relative size information when considering the accuracy you're trying to achieve. In injection molding, under high tonnage and pressures, you can't get thermoplastic to flow into 0.001" thick cavities or cracks. So at low pressures, like our printers, don't expect a 0.002" (0.05mm) layer to turn out very good in FFF printing. A fine layer is 0.1mm. There's tolerance in everything from the machined parts to the type of plastic to the PTFE tubing, etc. You have to account for those tolerances and design them into your finished product or 3D print. Not to get side tracked on a whole separate discussion, just a quick reminder that there's a bunch of variables in 3D printing that can make it tricky.
Here at the shop, not one of us have put ferrite on our machines. I agree that ferrite can't hurt. If miaviator was in house at SeeMeCNC, my team would say whoa, you changed too many things at once to make certain ferrite is absolutely necessary. We would try for the problem machine and change that one thing after observing the error to see the result. It's sometime painstaking to troubleshoot, but necessary. And it's very important to have good connections in the wiring of course. We've built a lot of machines and don't see a noise issue. So a wiring noise issue is likely corrected by the ferrite. It really can't hurt anything, but we're not convinced it's necessary.
Modifications are part of what this is all about too. I'm interested in some test results you guys post with and without the ferrite. Where are signal wires related to stepper motor wires? In the RMAX v1, running end stop wires up the tower with the extruder stepper wires guaranteed shifting layers. The current in the stepper wires induced a false signal in the end stop circuit. So keep your stepper and signal wires separated. This is why you do not probe with hot end on.
Are you probing with bed and hot end on? Then you're probably not running current firmware or your firmware is not configured properly .
I2C bad. No way. Nearly every Eris and RMAX v3 machine built at the shop prints great with a very good first layer after firmware upload and auto probing. The repeatability has even surprised me. Some of this error may be caused by the mechanical build. See my link above for mechanical build notes that can improve your results.
Look for a *possible* firmware update at the end of this week