I'd suggest you to check all of your ISRs. Are all of them assigned to appropriate vector? e.g in case your original HC08 interrupt routine is declared as:
void interrupt MyISR(void) { .... }
and the routine is assigned to appropriate interrupt vector in the original .prm file e.g.
Vector 13 MyISR
then this information is not passed into CFv1 project and a "Porting Tip" may be generated. It's recommended to use rather: