Everything Fernando said it exactly right, but your problem is a
common on in pre-CVS matlab. FYI, Here is what is happening. It
appears you have previously plotted some nonpositve data. pre-CVS
matplotlib maintained the data limits as min/max for y and y which it
uses in the autoscaler. CVS matplotlib keeps track of min, max and
min-positive so the log autoscaler can do the right thing.
It also implements lots of other log fixes and optimizations. Once
this last bug is hammered out, we hope that you won't be able to break
matplotlib (in agg, other backends haven't ported the new changes yet)
with log plots, with the possible exception of plotting *all*
nonpositive data. But if do that, you deserve what you get 
JDH