Dear Friend,
I have read your post. I understand that still you are treating as a consultant. as per appointment letter your extension period is 3 months from the date of appointment, however they might have extended another 3 months of your probation period. Please read thoroughly your appointment order and check whether is their any clause stating if we are not satisfied we may extend your probation period without any prior information.
About your IT deductions, according to Income tax norms under consultancy (194J) head if payment is Rs. 30,000 or above in particular finance year tax to be deducted @ 10% and if paid previously TDS to be deduct TDS on entire previous payments ( previous payments means particular financial year payments) as per norms. In your case they might have paid below Rs. 30 k in first three months. The movement you attain or crossed Rs. 30k they have deducted @ 10% on total payments which is right according to Income Tax norms.
About your concerns I am giving brief answer as per my view.
1) As a consultant you should comply your company polices .Because you might have singed on appointment letter copy. This means you have agreed and you are going to follow the company polices.
2) When company selects a Person and wants to hire him, company has to issue appointment letter. In your case company did the same, here there is no question of null and void.
3) Form 16 is issue only for regular employees not for consultants, in your case you are entitled for Form 16A. I hope they will issue form 16A (tds certificate) since they have deducted tax from your consultancy services.
4) You cannot ask your accounts department people for non deduction of TDS, since they are complying and deducting tax as per IT rules. Note that it is a statutory obligation.
5)May be they might have told you that you will get total amount at that time of appointment. To my knowledge in appointment letter they might have included the clause that taxes are applicable according to statutory norms so read thoroughly your appointment letter. Generally we don’t know about taxes at that time of joining, this is where we fall in to soup so we should be more careful in this kind of situations.
In your case to get refund you have to submit Income Tax Returns .
As a consultant you can claim few of your expenditure like conveyance, Fuel, depreciation of vehicle (if applicable), Telephone charges, Rent etc.These all expenditure can deduct from gross income with result your total Income will reduce. Apart from this you can show your savings like LIC, Mutual funds, P.P.F etc U/S 80C upto Rs. 1,00,000/-. I would suggest you better consult Tax consultant or practicing Chartered Accountant for submission of Income Tax, returns they will guide you in proper way.
I hope you are clear now.
I wish you all the best & God bless you .