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S3D first layer height
So I have determined my issues with bed height is from the s3d slicer. My first layer height is 30%. Which should be a layer offset of .6mm since my layer height is set to .2mm.

Well what happens is my nozzle height is set to the bed height and s3d sets an offset of about 1.1mm which throws off my first print layer. The weird thing is yestersay I wasn't having any issues. It was working perfectly. Today, now that I booted my pc back up the first layer height is incorrect. Does anyone know why this happens, if I don't get a response I guess I'll have to visit the s3d forums.
While I dont know why it would happen, couldnt you offset Z in s3d settings to compensate for whats happening?
It was from first layer height. If I change my layer height to something more than .2mm I need to lower the first layer height % for it to work.

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