Z Probing and Print issues(not like the norm)

So Ive enabled auto bed leveling and have set my offset for Z probe within the slicer settings. Im using marlin Firmware with ramps 1.4. If you see the attached screen shots, you can see a normal model before slicing, but after slicing it drops the print below the print bed. This does not cause a print head crash, rather it skips those layers, In this particular model 49 of them, And it reflects like wise in the print. If i watch the status bar at the bottom of the screen, the info reflects incorrectly as well. It seems to print one solid layer and then Straight to infill but the solid layer is so thin its more like a raft(.1mm layer height)

I dunno what to do about it. Ive tried readjusting the Marlin offset, checked through Repetier for something, and googling this problem but i have found nothing. Thanks everyone.

Im going to try and remove the Z offset in slic3r settings and add it to my firmware setting. If i remove the z offset in slic3r my print previews move back onto the build plane. will update on how it goes.

Is this possibly a bug within Repetier/Slic3r? Can somebody else verify in their settings?

Edited 1 time(s). Last edit at 12/15/2015 09:21PM by Tukr.

It appears that was the solution. Somewhere along the line during this setup up i may have mistaken the term repetier firmware for repetier host, or it may have not been that specific. Is this a bug in repetier/Slic3r though? Shouldn't I be able to set an offset in slicer and not have prints become partially flawed?