ISPManager have regular problems c DKIM. True. And, tried on different systems: CloudLinux (including other rhel-based system), on Debian and on FreeBSD. Two months ago was, well, a lot of problems. Out of the box did not work, only dopilivat hands. You know, with the policy of product development from ISPSystems it is not necessary to wait for the fixes. Moreover, they stated that working on the fifth branch of products, in the fourth only closed bugs. And, by the way, very slowly.
My advice: if possible, go to opensourcenow socket vestacp.com
developer with Habra. Incidentally, such problems were not observed.
And here, in your case, it is necessary dopilivat hands. Besides, the information provided is not enough to say for sure what the problem is.