Solved Starting layer height strange.

Hello all,
Recently installed the E3D V6 to my Robo 3D R1 +plus, absolutely love it. Followed Mike Kelly's how to guide an was relatively simple.
I have switched to using ABS from PLA and done fairly well. Prints come out fine and amazing quality each time with both PLA and ABS, one thing that is odd though is my Z offset seems a bit extreme.
I have been careful to get this set, and done bed calibrations but it seems I have to keep the Z axis offset between -0.40 and -0.35 for anything to be squished to the bed otherwise it is printing off of the build surface and obviously nothing prints.
I use Simplify 3D for my slicer program and to run the printer when I am not using a Raspberry Pi 3 with Octoprint as a print server.
Can I adjust where the printer believes the build plate surface to be at the start so my offset does not have to be this extreme or am I better to just continue as I have been?

 

Thanks for the info!