Actually there are two issues:

1. The CalculationSS, CalculationConfiguration & CalculationMS files (accessed from FusionCharts LearnerKit)did not obtain the $$CurrentDir from FusionCharts Library, which I have assigned http://myservername/fc/charts in the script InitializeFusionCharts. Once I put the same calculation formula in the CurrentDir field in these files, they worked.
2. The GeneratingMultiCharts had the problem to display the right hand side chart (Year-Wise Sales Chart). It worked in the non server environment. Once I added the sort record script (sort by year, without UI) before displaying the object, it worked as expected.

Sorry I have posted my issued in a wrong forum previously.

FileMaker Server 9.03 Advanced on Windows Server 2003, Single Machine Deployment
FileMaker Pro 9.03 Advanced on Windows XP SP2