It should be the date of joining and not the date of confirmation that should be considered for deciding the eligibility and calculating the amount of gratuity. It is okay if the training period was apprenticeship under the Apprentice Act, but in a pharma company I don't find any scope for apprenticeship training.
The companies can't have their own rules for payment of gratuity and other statutory payments like bonus. It is settled law that the period of training other than apprentice training should be considered as service period for all the purposes, like gratuity, bonus, leave with pay, contributions and coverage under PF, ESI etc and there cannot be any exception to it also.
It is surprising that the claim for gratuity is not made even after 14 years of your leaving the organisation. However, the obligation to pay is on the employer and therefore, if you file a compliant before the appropriate authority, you will get it with interest.
Regarding payment of bonus, since it is based on profitability of the company and the employer is under no liability to pay bonus to employees whose salary is more than Rs 10000, (it should be Rs 3500 in the year 2000, I think!!) you can not take it as a right.
Attached is the form N which may be filed before the Controlling authority, Labour Officer in the jurisdiction of your company.
Madhu.T.K