The radius logs (/var/log/freeradius/radius.log) would say..
Wed Jun 29 15:26:10 2011 : Error: [sql] Couldn't update SQL accounting ALIVE record - Column count of mysql.proc is wrong. Expected 20, found 16. The table is probably corrupted
Thu Jun 30 03:32:01 2011 : Error: [sql] Couldn't update SQL accounting ALIVE record - Cannot load from mysql.proc. The table is probably corrupted
The fix was relatively simple once I found it. On the mysql server do this:
root@sql-server# mysql_upgrade --force
It fixed some issues with the table and after that my freeradius server started updating the acctstoptime again.