I'm not too sure if it's directly related to updates, as there isn't any sort of "history" for when an update has or has not been run.. as long as the binaries work, the reset should happen the same way.
As for systems where the reset does not happen, there are a few steps to check to see what's going on.
First check:
/var/log/cron
to check for the action=reset&value=all command.. ensure it's showing up on the first of the month, I believe it runs at 4:00 am.
Then beyond that, this is a somewhat related guide to check through:
http://help.directadmin.com/item.php?id=107
Also check to see if you've got any large backup commands being run at around the same time. If for example, the backups are issued at 4:00am, or slightly before 4:00, then if the backups are processed for the reset, should anything go wrong in the backup, the reset command may get "lost" if the dataskq process errors out. This a theory, and have not seen the dataskq do that, but just something to try.. (change backup times) to rule out, or verify it as a potential cause.
John