Jeez, where do I even start. This problem made me quit 3d printing for about 6 months and still plagues me to this day. My printer is a Printrbot Simple Metal. In the back right of the print bed the nozzle digs in to the bed causing tape to rip up and the print to fail. In the front left of the print bed it prints so high that it doesn't even stick to the tape. No, my print bed is not warped. I had this problem when I used a plate of mic6 aluminum and now I am using the Matrix Precision XY upgrade and have the EXACT same issue.
If this is of any relevance, my printer homes to the back right but when probing with G30 after homing all axes it returns Y=MAX rather than Y=0, and when I have the printer go to Y=1 from homing all axes it moves towards me 1mm (WHAT?). I'll post some numbers to show what I mean.
From cura I press home on X, Y and, Z then use G30
> G30
< Bed Position X: 0.00 Y: 203.20 Z: 0.40
< echo:endstops hit: Z:0.40

Now I send the X axis all the way over to the end and use G30 again
> G30
< Bed Position X: 190.00 Y: 203.20 Z: 0.05
< echo:endstops hit: Z:0.05

Now I move Y towards me and keep X in the same place
> G30
< Bed Position X: 190.00 Y: 13.20 Z: -0.97
< echo:endstops hit: Z:-0.97

Now I move home X and keep Y towards me
> G30
< Bed Position X: 0.00 Y: 13.20 Z: 0.55
< echo:endstops hit: Z:0.55

Now I run G29 (pretty much the same thing)
> G29
< Bed x: 10.00 y: 193.20 z: 0.34
< Bed x: 10.00 y: 10.00 z: 0.55
< Bed x: 193.20 y: 10.00 z: -1.03
< echo:endstops hit: Z:-1.03