There are two possible problems while loading Lotus Notes Web sites.
First, you may notice that many pages are not loaded at all, probably because of improper Project settings. Please open the Project Properties dialog and ensure that the File Filters | Other category is checked. This will allow loading files with .nsf extensions and many other pages that do not have an extension.
Secondly, some pages could be referred as both files and directories simultaneously. Portable Offline Browser currently cannot handle this problem. We plan to address it in our next release.