This may be a big noob question, but i can't find a definite answer to this;
As i understood you gain rep with your guild by doing quests, killing bosses and the likes but there is a weekly cap for the max rep you can gain.
I myself are somewhat into friendly but others are honored already with our guild.
Does the cap only apply to rep gained from quests then?
I'm a bit lost here.
Yep, the cap reset at 3am after the game launched. So basically some guilds/players got to do hours of experience/rep earning while others that didn't get to play until 3am (or even later) didn't get that bonus period of time. It's very possible that you're seeing a result of that.