Benefits of Project Based employee

I would like to ask some matters about my employment.

I was hired as a Project-Based Employee last 2007 for a one (1) year duration. After one (1) year it was renewed yearly until 2010, but after my 2010 contract expired, my employer had me sign a new contract with salary increase 5% of my basic salary. But the said contract was lost by our HR Legal Department and the Management was not able to sign the contract. After too many follow-ups and chasing the HR Legal Department, nothing happened and the salary increased was not imposed. This year (October 2012), the management let me signed a new contract without mentioning anything about the lost contract and the unimposed salary increase. I signed the contract because they might just fire me if I insist on mentioning about the lost contract.

My questions :

1. Do I have the right to demand for backpay even if the contract was lost and the President was not able to signed because of the HR Legal Department carelessness of losing the contract?

2. Should I be already a regular employee since this is my 6th year as Project-Based Employee?

3. Am I entitled for other benefits like the regular employees have? For 6 years as Contractual Project-Based Employee my benefit is only the 12 days vacation leave and nothing more.

4. I am a Project-Based Employee, but the job I am doing is not a project but a job of a regular employee. Is my employer violating any labor law with regards to this?

I hope you can enlighten me on this matters.
Thank you very much in advance!

Love Peace and Gratitude,
Sen Iris Villamor