Please pass this on to your developers:
In the core.charts.StackedColumn2DChart file (version 3.1 - ActionScript ), on line 477, you are commenting out the following code:
this.params.yAxisMinValue = atts["yaxisminvalue"];
There is a comment above this line that users cannot set the yAxisMinValue since it always emanates from 0. Although this may have been true in your previous version of FusionCharts, it is certainly possible to have a stacked column 2D chart with both positive and negative values in the same column in your current version of FusionCharts. I have uncommented this line, and now I get the appropriate behavior when I set the yAxisMinvalue for this chart. You should 'fix' this by uncommenting the code in the next release of FusionCharts.