ASP.NET, SQL Server, WPF, C#, VB.NET

Hi,  
  
My desktop application publishes web pages to an FTP location.Its using  
  
CFTPConnection MFC class. IIS 6 server is used for FTP.  
  
I'm able to open .htm files generated on FTP location, these files are with  
  
UTF-8 encoding. The problem is where there is link with href to a javascript  
  
function nothing is happening. If I publish this to local location & open  
  
with http everything works fine.  
  
Not getting reason why javascripts are not getting called in herf in html  
  
file on FTP location.  
  
Is any setting missing?  
  
Thanks