If you are using a COM object that opens windows or dialogs (like Office applications), those windows or dialogs will not appear and will stay invisible even if you use codes like     

$word->visible = true;

To solve this problem, go to the web service properties (Administrative Tools) and click (in the Logon TAB) "Allow the Service to Iterate with desktop".

This explain lots of problems to close applications. When you try to close, the dialos asking to save the file must appear, but only in the option to iterate with desktop is on.

Hope it helps.