Running cron results in Caches Flushed
system_cron calls cache_clear_all with $cid == NULL, which should just be clearing out expired entries.

My guess is that something else is wrong with the system, and cron is failing as a result.

When you upgraded, did you make sure you ran update.php?

Do you see cron listed as being run in watchdog (/admin/reports/dblog)?

Are there any php or other errors/warnings in watchdog around the cron run?

What does your search index status say (/admin/settings/search)?  cron will index search each run.  If this takes too long, you may have problems.  Try dropping down the number of items per run.

If you run drush cron from the command line, does it run properly?