mmorel,
I am not against you clarifying this with HR, but I think you misunderstood the "payment in lieu of - Notice Period (90 days)". The 5% is included in that payment which I assume would be your contribution. The company's share would be 10%, as far as I know since I check my ISP contribution every month.
You might be wondering why they didn't pay this 10%-company contribution to you (for this 90 days notice period)? My only answer is because of the "Payment in Lieu of" notice period. You don't really have a case regarding this, as you have been paid for that 90 days in Lieu of your services, meaning you can and you may leave the job without having to work for this 90 days. That's probably contrary to your understanding, but if it so, you may email them and find out yourself. goodluck