After battling with the problem for a long time it solved itself for unknown
reasons and the links do not require http:// in front of them anymore.

However, I copied and renamed the whole directory and changed the links
contained in the link list, and now receiving the same www.domain.com!=primary
error. Only this time, I have not been able to fix it by adding a http://
prefix to the links.

The httrackrc is exactly the same notwithstanding changed rules. Httrack.exe
fails leaving hts-in_progress.lock behind.