We had the same problem.
The solution we have come up with is relatively non-intrusive. Your latex code stays the same, no additional special tags, but your x co-ordinates of your negative values changes a little bit.
Since every x co-ordinate by default is stacked separately, we would plot the positives at e.g. 1, 2, 3, etc and the negatives at 0.999, 1.999, 2.999, etc.
For the human eye, it would appear to be directly on top of each other (if not, add another 9), but for purposes of stacking, latex will stack them separately.

(source: pnpscada.com)
here is a code extract of the .tex tile:
. . .
\begin{axis}[width=20cm, height=9.75cm,
scaled ticks=false,%
%bar width=5pt,
xmin=-0.15,
xtick={1,...,\days},
xmax=\the\value{daysp}.15,
ylabel=energy in \si{kWh},
xlabel = date,
%xlabel= {\yearnow},
%xtick align=center,
%xticklabel style={rotate=90,anchor=east},
grid=major,
legend cell align=left,
%legend entries={baseline,target,trend,low demand--off-peak,low demand--standard,low demand--peak,high demand--off-peak,high demand--standard,high demand--peak},
legend style = {area legend,legend columns = 4,
%legend title = legend,
at={(0.5,-0.12)},
anchor=north},
%legend entries={baseline,target,trend,low demand--off-peak,low demand--standard,low demand--peak,high demand--off-peak,high demand--standard,high demand--peak},
title={{\month} {\yearnow} consumption for \meter},
%title style={at={(0.5,1)}},
ybar stacked,
set layers
]
. . .
\trend ;
\addplot[draw=black, fill=color8, forget plot] table [x=x,y=v8]{Month.csv};
\addplot[draw=black, fill=color1, forget plot] table [x=x,y=v1]{Month.csv};
\addplot[draw=black, fill=color12, forget plot] table [x=x,y=v12]{Month.csv};
\addplot[draw=black, fill=color6, forget plot] table [x=x,y=v6]{Month.csv};
\addplot[draw=black, fill=color9, forget plot] table [x=x,y=v9]{Month.csv};
\addplot[draw=black, fill=color3, forget plot] table [x=x,y=v3]{Month.csv};
. . .
and an extract from a similar Month.csv file (not exactly the same as the picture, but it shows the idea) (columns are tab delimited):
x v7 v8 v1 v2 v11 v12 v5 v6 v9 v10 v3 v4 target
. . .
6.25 0 0 0 0 0 0 0 0 0 0 0 0 1682.16
6.5 0 0 0 0 0 0 0 0 0 0 0 0 1682.16
6.999 0 0 -30 0 0 0 0 0 0 0 -54.500 0 1682.16
7 0 0 0 200 0 0 0 0 0 0 0 1190.000 1682.16
7.25 0 0 0 0 0 0 0 0 0 0 0 0 1682.16
7.5 0 0 0 0 0 0 0 0 0 0 0 0 1682.16
7.999 0 0 -50 0 0 0 0 0 0 0 -93.000 0 1682.16
8 0 0 0 400 0 0 0 0 0 0 0 1068.000 1682.16
. . .
ybar stacked? Perhaps what you are looking for is justybar? – Peter Grill Apr 30 '12 at 17:38stackedis that the "bar is drawn from the top coordinates of the previous bar". Since you have negative coordinates, the bar is drawn downward from the top of the previous bar exactly, and hence the overlap. Still not sure I understand what you want. Perhaps if you posted an image of the desired solution it would be clearer (even if you have to manually tweak the coordinates, to be able to show the desired result). – Peter Grill Apr 30 '12 at 18:09