Yeah, no clue about that. ISPCONFIG is not being touched when it happens. Usually, it's at random hours of the day when I'm out on the down, meaning no-one is using SSH or ISPCONFIG.
Then the theory that you posted about the reasons for the segfaults can not be the case. If you are not logged into ispconfig, nothing gets changed or altered in the tables used by mydns. You should tell the guys in the mydns mailinglist that the segfaults happen when no data gets altered or added in the database.