At our web host they've turned off the SpamAssassin auto-update because of this problem. It was too much of a hassle that every time the auto-update ran it turned off SpamAssassin and they had to go through and manually turn it back on. So now we have SpamAssassin 3 running fine - just no auto-updates until this gets straightened out. They feill this may be the best solution for a while.
The alternative I see is a cron job that turns it back on periodically or ideally is triggered by the auto-update. Perhaps it could be triggered by detecting that SpamAssassin is no longer marking messages - e.g., ever hour it would do a test message, see if SpamAssin marks it and if not then turn on SpamAssassin.