Firmware Bug? Bed Level Correction
Ok, so went through the manual and in section 6.3.9.1 Bed Level Correction (Kit Only), it says you can virtually lower the bed using -20 microns on the side that is too high. However these micron corrections are doing the opposite.
What I have found is that the Bed Level Correction numbers indicate how much more/less space you want between the bed and the nozzle. So if you are squishing too much on one side, you want to use a positive number to increase the distance between the bed and the nozzle.
Once I figured this out, it was so much easier to get the bed leveled nearly perfectly.
Also, try using the calibration squares .stl instead of using the Prusa nameplate. Makes calibrating the sides much easier. Just remember to zero any Bed Leveling you have done and first get the center square the way it needs to be. Then make adjustments to the sides that need it. You can only adjust the center by using Live Adjust Z, so getting that right first is necessary.
http://www.thingiverse.com/thing:1776031