Hello,
I decided to post this fix after searching online for a solution but could not find one except to rebuild ISE.
*****Issue***
ISE will not accept any configuration commands, or application start/stop commands even after restarting several t...
****Solution ****
At the command prompt, enter "application configure ise"
select "[5]Refresh Database Statistics"
select "[19]Exit"
This would stop the DB process and allow you to input your commands. I hope this helps.