php script repeats itself while running on postgresql

I run php script which select/insert to postgresql database.

The problem is that when i run the script to select more than (400000) rows,

the script repeats the insertion for the same rows!

I found this error in postgresql log :

2014-12-21 13:14:53 AST LOG:  checkpoints are occurring too frequently (7 seconds apart)
2014-12-21 13:14:53 AST HINT:  Consider increasing the configuration parameter "checkpoint_segments".

i changed the configuration to be :

- Checkpoints -
checkpoint_segments = 100       # in logfile segments, min 1, 16MB each
checkpoint_timeout = 1h     # range 30s-1h
checkpoint_completion_target = 0.9  # checkpoint target duration, 0.0 - 1.0
checkpoint_warning = 30s   

 # 0 disables

but the problem still occurs. can anyone let me know how to fix this?