Could you please add few details?
This topic is related to S12P. Correct?
By “Time interrupt” you mean RTI, TIM, API,…?
By “period of Time interrupt” you mean just first period after wake-up, or all periods after wake-up?
What you set as clock source for your time interrupt?
I can imagine case when you use PBE mode (busclock=oscclock/2) and MCU wake-up from full stop mode. In that case will be PLL enabled automatically (PLLSEL=1) and after wake-up you should wait for UPOSC flag (oscillator ready) and clears PLLSEL bit back, otherwise you will get different bus clock value.