I had the same problem.
/var/log/dist-upgrade/20090625-1834/main.log (to 9.04?) contains: 2009-02-07 16:37:45,999 DEBUG disabling apt cron job (0100755) 2009-02-07 20:49:12,595 DEBUG enabling apt cron job
/var/log/dist-upgrade/20091213-2027/main.log (to 9.10?) contains: 2009-06-25 19:37:59,096 DEBUG disabling apt cron job (0100755) ...but doesn't contain a corresponding "enabling" message.
I had the same problem.
/var/log/ dist-upgrade/ 20090625- 1834/main. log (to 9.04?) contains:
2009-02-07 16:37:45,999 DEBUG disabling apt cron job (0100755)
2009-02-07 20:49:12,595 DEBUG enabling apt cron job
/var/log/ dist-upgrade/ 20091213- 2027/main. log (to 9.10?) contains:
2009-06-25 19:37:59,096 DEBUG disabling apt cron job (0100755)
...but doesn't contain a corresponding "enabling" message.