I'm new on using Hibernate so please be bare with me.
Currently I'm using : Netbeans 6.8, MySQL 5, and Hibernate3 with POJO model

I've got a problem which I can describe as follow:
A part of my application is supposed to insert a record to a specified table.
Each record in this table is unique, hence there is a check before inserting the record to find out whether the data is already there in the table.
If it does not exist then the data is inserted, otherwise it won't be inserted into the table.
It works fine.
But then, if I remove a record or all record on the table outside the application scope ( using MySQL command line to delete all records in the table ) the application fails to detect that the record does not exist anymore after deleting.
It keeps saying that the record exists.
It seems that Hibernate persists the query to check for existing record somewhere.

Well...I know I need to dig more about Hibernate :D but meanwhile please enlightening me
TIA

Could be caching issue. You can try one of these suggestions, see if the that help:
Set the first-level and second level cache usage to false in the hibernate config file.
Flushing and clearing the session after every insert.

Things that can help:
Override the equal and/or hashCode method in the entity class.

Also to skip to procedure where you have to query the table every time you are inserting the data to see if it already exists, try overring the hashCode method in the entity class. create a hashCode based on some criteria using data you get when you populate the fields, and then setting that as the primary key, since the criteria will always produce the same hashCode if the data is same, at which point you can either skip it, give an exception, or simply update the record

As the previous post by ivrirani said it is likely a caching issue. Hibernate has several different caches. The first-level cache is bound to the session and is mandatory (it can't be disabled it the config file!). The second-level cache can store both entities and query results. The second-level cache need to be configured in the configuration file and for each entity that should be stored in it. Query results can be cached by calling Query.setCacheable() before executing it. Overriding equals() and hashCode() will not affect how things are cached.

So... since the information you are looking can be cached at various places in Hibernate it is hard to give any more advice without seeing your code and without knowing more about your configuration.

Yes, it was a caching issue and somehow I put incorrect flow to get the session close to make sure the next query will read fresh data instead of from cache.
Managed to get it solved :)
Thank you very much for replying.