Can you share which 5.4 version they have running, and what kinds of weird behaviors they're having? That would probably help others. I have a 50E+5.4.3 running since earlier this year but so far no issue I encountered yet although I need to admit it has no UTM stuff activated.
3 Issues - We got locked out of one when upgrading. and had to reboot it, but have no idea why. That unit also dropped packets that are directed to the box, we will not put it into production until TAC can tell us why and what needs to be done. We went from 5.4.1 to 5.4.2 and in typical TAC function they will likely tell us to go to 5.4.3 without any further trouble shooting.
The other unit at another customer will not negotiate or allow us to lock the speed to the switch at 100 Full, it keeps going to Half - when we set it to full the port does down. No it is not the switch as there is a 300D right beside it that works even in the port that the 60E does not.
And Lastly we have a 60E on a 150Meg Circuit that for some reason we can't get more that 80 Meg throughput out of.
My company has delopyed well over 100 Fortigates from 60D all the way to 1000D's and I can tell you that these units are not ready.
I've deployed two so far, both with 5.4.3 code (haven't touched earlier revisions of 5.4), replacing a 60D and a 90D and I'm very much impressed with the deep inspection performance - policies that crushed the previous boxes are barely even felt now. Haven't encountered any show-stopping bugs as of yet.
Recently I replaced the 60D unit to 60E unit. I see a huge improvement in performance. Regarding issues - there are some, but in my case are not burdensome (5.4.2). The only thing that bothers me is two times more memory consumption. After a month the average memory usage is 64%. Fortinet support claims that it is a normal condition.
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