I have worked with your requirements and like to share that if you set all the values for a particular series to blank then presentation gets corrupted. An issue with ID 30981 has been created to resolve this issue. As a workaround, if you set any one value inside the series to 0 or some other value then presentation generated is fine. I feel if you set the value of any one series item to 0, then you can still achieve the results. I have used following code snippet as workaround.
//Instantiate PresentationEx class that represents PPTX file
PresentationEx pres = new PresentationEx();
//Access first slide
SlideEx sld = pres.Slides[0];
// Add chart with default data
ChartEx chart = sld.Shapes.AddChart(ChartTypeEx.ClusteredColumn, 0, 0, 300, 300);
//Setting the index of chart data sheet
int defaultWorksheetIndex = 0;
//Getting the chart data worksheet
ChartDataCellFactory fact = chart.ChartData.ChartDataCellFactory;
//Delete default generated series and categories
chart.ChartData.Series.Clear();
chart.ChartData.Categories.Clear();
int s = chart.ChartData.Series.Count;
s = chart.ChartData.Categories.Count;
//Adding new series
chart.ChartData.Series.Add(fact.GetCell(defaultWorksheetIndex, 0, 1, “Series 1”), chart.Type);
chart.ChartData.Series.Add(fact.GetCell(defaultWorksheetIndex, 0, 2, “Series 2”), chart.Type);
//Adding new categories
chart.ChartData.Categories.Add(fact.GetCell(defaultWorksheetIndex, 1, 0, “Caetegoty 1”));
chart.ChartData.Categories.Add(fact.GetCell(defaultWorksheetIndex, 2, 0, “Caetegoty 2”));
chart.ChartData.Categories.Add(fact.GetCell(defaultWorksheetIndex, 3, 0, “Caetegoty 3”));
//Take first chart series
ChartSeriesEx series = chart.ChartData.Series[0];
//Now populating series data
/*
series.Values.Add(fact.GetCell(defaultWorksheetIndex, 1, 1, 20));
series.Values.Add(fact.GetCell(defaultWorksheetIndex, 2, 1, 50));
series.Values.Add(fact.GetCell(defaultWorksheetIndex, 3, 1, 30));
*/
series.Values.Add(fact.GetCell(defaultWorksheetIndex, 1, 1, “”));
series.Values.Add(fact.GetCell(defaultWorksheetIndex, 2, 1,""));
series.Values.Add(fact.GetCell(defaultWorksheetIndex, 3, 1, “”));
series.Values.Add(fact.GetCell(defaultWorksheetIndex, 4, 1, 0));
//Take second chart series
series = chart.ChartData.Series[1];
//Now populating series data
series.Values.Add(fact.GetCell(defaultWorksheetIndex, 3, 2, 0));
ChartDataCell cd = chart.ChartData.ChartDataCellFactory.GetCell(0, 1, 2);
cd.Value = “”;
series.Values.Add(cd);
cd = chart.ChartData.ChartDataCellFactory.GetCell(0, 2, 2);
cd.Value = “”;
series.Values.Add(cd);
cd = chart.ChartData.ChartDataCellFactory.GetCell(0, 3, 2);
cd.Value = “”;
series.Values.Add(cd);
cd = chart.ChartData.ChartDataCellFactory.GetCell(0, 4, 2);
cd.Value = 0;
series.Values.Add(cd);
// Save presentation with chart