Hi there
Look like your extruder is not working as it should - From what you said.
But, before you make any further moves, please upgrade your Firmware together with your desktop into latest version FW 1.7 DT 3.6)
Then unload filament completely and make sure your nozzlehead is moving freely up&down. Don't press directly into nozzle tip!!!
Then only make your Level build plate again.
Should be OK now.

But if it is not OK again - then your extruder is not reporting correctly while Level build plate procedure is done.
In this case, You can stil make it work of course with a little trick - get yourself buisness card, wait for print procedure to start and put that business card under nozzle just before it get into center point of build plate.
This way you will arteficialy make your build plate a bit higher and nozzle won't punch into build plate at start of printing.
It might print too high ...