Is it ok to report a bug even if you don't know that for sure?
Yes.
Just to be clear when you upgrade you don't have to restart any jails and your DDNS service still works?
True statement. The upgrade will reboot FreeNAS and your system should come up normally.
So your suggesting wiping out my HDDs and make like I just build the FreeNAS box?
No! I'm suggesting you just delete your jails, not your pool. I don't know how many jails you have but I think this is the long term solution.
It took me a long time to get everything working, I'd be afraid of not getting it all setup again.
You should record all the setup info such as user account, IP addresses, all that stuff. Ensure that you have a backup of your configuration file and if all fails you could just restore it however if you delete your jails then that would not be restored of course. Also if you do this, ensure you delete the jails template as to force the newst version to download.
But if you would rather leave your system as-is, that is fine too and you could do this once you are ready for it. I was only suggestion options to fix the problem but it sounds like you are fine with manually starting your jails. Also, if you upgrade to FreeNAS 11, there is a possibility your jails will not work at all, just a note of caution.
Good luck with whichever path you choose.