Hey Jonathan thanks for posting this thread, because I am having the same problems (not as bad but it's close). I thought it was a firmware issue and was trying to resolve it that way. Turns out my motherboard is one of the bad ones and needs something extra to be updated, so I'm kinda stuck-like-chuck.
I'm wondering if that's the same issue with yours and the mobo is the actual problem. Have you tried updating the firmware?
I really don't understand how it could be the z-axis. I think the motors are over stepping and building entire layers wider than the last.
I would think if it's a wobble in the z the layers would look like:
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----------------, and every layer would be equal but just not even, and not like:
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----------------, where every layer is either building larger or getting squashed more by the extruder.
I think the effect on the first few layers are lessened due to the heated bed. The farther away it gets from the heat, the more pronounced the problem is.
I also thought it could be that the nozzle is loose and wobbly as it drags over the extruded plastic but I tightened the wooden plate and that also didn't help.
...or maybe it really is an issue that this guy brought up on my non-solution to z-axis wobble. (check the comments)
http://www.thingiverse.com/thing:36177 (BTW, thanks Ian for clearing up what I couldn't.)