Before you moved to PMS in 2006, you would have received a global sum under the GMS contract. Certainly, a practice receiving funding under the GMS contract would not receive any additional funding to meet the employer's superannuation.
The question of whether the PCT should be funding the employer's superannuation contributions under PMS is dependent on the exact PMS contract it signed. So you need to examine this carefully and challenge the PCT if it appears that the superannuation funding should be higher.
Both GMS and PMS contracts provide a budget framework which, with the exception of seniority payments, is unaffected by the delivery of care in terms of the number of GP principals, salaried doctors, nurse practitioners or non-GP principals.
A partner who has taken 24-hour retirement has made a personal decision not to contribute to the NHS scheme and this does not affect the practice's NHS contract income or the other partners in the practice in any way, either positively or negatively. So the baseline funding should be divided in profit-sharing ratios with the partner who has taken their NHS benefits entitled to take the appropriate portion of the employer's superannuation funding given that it is paid to the practice as income funding.