Suitecrm repair and relationship issues

We are facing many time timeout issue. We have set all possible php_value with proper data, I mean at possi9ble highest value.
i.e; max_execution_time =6000
and uploaded_size also at proper but stil no luck

Why suitecrm creates such issues many time ?

please provide common solution for this problem.
There are so many solution in this forum , but no one is working in our case.

Please provide proper solution.


What are you doing when it times out?