Ok, so after some more investigation I decided to revert back to 378.56_2, the old FW. Reasons why is that when I left it on for like 2 hours I got the same effect as with the new FW. The reason for the same effect is (what I think) that the CPU can't handle the traffic and the continuous downloads from my server + the traffic from all the visitors. I have a ASUS-AC66U, and it's a good router, but the traffic is just to much to handle without NAT Acceleration so the effect became that the site was offline as before - sometimes it worked, and some not, but mostly not.
With the old FW I have no issues at all, and since I now tested several times (did some tests before as well) my decision is to use the old FW. Please fix this irritating bug in the next release! Thank you.