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Posting to say that I have the same issue here. Thinness/no print on the y-z side and thickness on the x tower. I squared all my towers as best I can but the problem did not fix itself.

Edit: v3

Just wanted to say that using only three bed clips, with a washer under each and the smaller calibration radius, my V3 seems to calibrate extremely well now and I get very good first layer results.

I do have an enclosure on mine which will definitely make it more rigid and may be helping some.
http://www.thingiverse.com/thing:1796438

Just wanted to add in, I am seeing a similar issue on my v2 with the he280 installed. I am getting an extremely thin first layer between the z and x axis.