PF dues

I have a problem on which i need some legal views.

My company employed few people in oct 2006 and started deducting PF pending registration with PF authorities. Important fact to note is contract letter mentioned that PF amount will be deducted from their salaries and equal amount will be contributed by the company. Now PF authorities alloted registration from Oct 2007 . The company wrote many letters to PF authorities requesting for advise on what to do with PF amounts as company cannot deposit the same due to lack of registration number for the said period.

So what should be done to PF amount
1.deducted from employees
2.contributed by company (and provided in liabilities)
3.PF admin charges (provided in liabilities)