Hi,
The Individual Rx Mask Registers can only be accessed by the CPU while the module is in Freeze Mode and MBFEN is set. Out of Freeze Mode, write accesses are blocked and read accesses will return “all zeros”.
So be sure the FlexCAN is allowed to enter Freeze mode (MCR[FRZ] set) and Freeze mode is really entered once you break debugger (FRZACK and NOTRDY flags set).
BR, Petr