Thanks for the suggestion cybershot , I was going to use a framework if I didn’t manage to solve this issue.
However, after spending some hours looking for code missing commas :), I FINALLY managed to figure it out.
The problem was in header.php, where i was calling for a global.js with some custom jq functions of my own. After commenting out that line, comments worked like charm; I renamed the file to another name, and no more problems with comments what so ever.
Maybe wordpress uses another file with the same name, or simply doesn’t like the name, I frankly don’t know.