Hi,
Most probably the issue is that a baud rate is not set similarly on both the JM60 and MPC5643L.
On the JM60 the baud rate is set as SCI baud rate = BUSCLK/(16xBR)
Where BR = 1 to 8191. Assuming the bus clock is 24Mhz, then you can calculate baud rates the JM60 can be set to:
BR=1 … baudrate = 1 500 000, bit period = 0.666 us
BR=2 … baudrate = 750 000, bit period = 1.333 us
BR=3 … baudrate = 500 000, bit period = 2 us
BR=4 … baudrate = 375 000, bit period = 2.666us
etc..
If you set the LINIBRR and LINFBRR registers of the MPC5643L's LINFlex module in the way you get a baud rate as close as possible to above values, then you should be able to communicate properly.
See chapter 30.12.3 Fractional baud rate generation of the MPC5643L RM to know how LINIBRR and LINFBRR values are calculated.
BR, Petr.