This happens because Portable Offline Browser has to rename certain symbols to make URLs compatible with the filesystem. On the other hand, the renamed URLs have to maintain ability to be reverted back to online form.

For example, ? symbol which often can be found in URLs have to be replaced with some other symbol (@). Otherwise a filename with the ? symbol cannot be created in Windows. The sequence of symbols _40 has to be replaced with _5F40, because Portable Offline Browser reverts _40 to @ symbol in an online URL.

In any case, all links in the downloaded files are correctly converted to match changed filenames, so you should have no problem browsing the site offline.