I am having this issue as well...
Running the following against a presentation that has a macro in it always prints "macro not present."
The saved presentation has no macro in it, despite the template containing one.
The exception leading to the catch block is not being thrown.
presentation = new Presentation(SystemInfo.getTemplateFileDir() + "\\Template.ppt");
presentation = new Presentation();
System.out.println("presentation has macros");
System.out.println("macros not present");
presentation.write(SystemInfo.getTemplateFileDir() + "\\TemplateTest.ppt");