Error: I have protected a web site that uses javascript to display pop-up pages but they are not displaying

The solution is to not protect the pop-up pages.

If the javascript code of the protected HSF file points to open a regular HTML pop-up page (or anything apart from a protected HSF page), then it will work fine. However, you must make sure that the unprotected pop-up files are there for IE to load them (so they must be copied across to the output folder).