Hi Otze,
What do you use the TIM for ?
Is it linked to LIN ? Because the ESCI has an integrated simple Timer.
What can happen from what you described is that your TIM ISR is too long compared to speed of messages and you get a Buffer Overrun. It means you get a new message when you haven't read/removed the previous one from the Data Register.
If the latest is the case and you need the TIM for something else, you need to have quicker TIM ISR.
Or you can also have the system having a greater bus clock so TIM ISR time is not significant compared a a LIN message.
Note that 9600 is quite slow and easily handled by an HC08QB8 which can be a LIN Slave node at 20kbps without the slightest glitch.
Cheers,
Alban.