Please check the postscript backend results regardless of whether the cntr.c change I suggested makes a difference or not; in fact, just try the different backend first. You could also try the png backend with a different dpi setting. Looking again at your plot, it looks a bit like a rounding problem, and I don't see how that would arise in cntr.c. It could still be a rendering problem and be related to the chunking; there might be rendering anomalies at the chunk boundaries. Cntr.c itself is still the prime candidate, though. The artifacts remind me somewhat of the bug I was working on; maybe in both cases, the tracing algorithm is turning left when it should turn right, or something like that. It might be something like a "<" that should be a "<="...
Near the very bottom of the Bz and some other panels there are some spiky features, different from the blocky artifacts that make stripes near 0.3, etc. Are the little spiky things in the data, or are they also artifacts?
Do the blocky artifacts correspond to your grid spacing--are they single-gridpoint offsets?
If you plot only a subdomain--a smaller range of x and y--do the artifacts remain?
Now, my first question is: notice the artifacts on the contours of Bz and I at y=0.3 and y=0.55, and on the contours of Q for multiples values of y. These doesn't come from data, as they disappear when zooming in. Do you know where do they come from ? And, more importantly (to me), how to get rid of them ?