I just looked through every single cron job (in /var/spool/cron) and none of them run anywhere near the times that it happens.
However, I have noticed a ton of crond processes at these times, I overlooked them thinking that they might have been piling up due to the lag but realise how stupid that is now. I will investigate them further.
Interesting thing is, it only happens when I have suexec enabled in litespeed? Everything runs perfectly on the server, but at these times everything seems to go crazy.