Well, I've hit a new problem with the log plotting issue. Try the following commands after 'ipython -pylab':
I get an apparently unbreakable chain of "Cannot take log of nonnegative value" messages for every following plot(), semilog(), or loglog() command until ipython is exited. None of close(1), clf(), or cla() helps clear the problem. Only creating a new figure with figure(2) and plotting to it seems to help.