Hi Jennie,
Putting main.c to new project is not enough. For proper flash operation you need to define RAMCODE placement in PRM.
Did you verify flash programming is working? Garbage in reprogrammed string? If it worked and still no problem on second run , then perhaps S12ZVFP and S12ZVCA are handled by CW differently.
Here's my screenshot from 2nd run. See where programming stops in console window.
Below is full contents of console, I'm not sure but looks like two runs are there, first with successful VC command and one with VC which sticks.
Regards
Edward

Starting 3rd party flash programming...
GDI: Mtwks Callback(MTWKS_CB_PROJECTACCESS, Section : STARTUP, Entry : SPECIFY_NETWORKCARD_ENABLED, Value : 0, R) => DI_ERR_NONFATAL
INF: Copyright 2012 P&E Microcomputer Systems,Inc.
INF: Command Line :"C:\Freescale\CW MCU v11.0\eclipse\..\MCU\bin\de.exe" -noni -language en -ORBendPoint giop:tcp:127.0.0.1: -ORBtraceLevel 0
GDI: Mtwks Callback(MTWKS_CB_PROJECTACCESS, Section : PEDEBUG, Entry : IS_GDB_CONFIG, Value : 0, R) => DI_ERR_NONFATAL
INF: CMD>RE
INF: Initializing.
INF: Target has been RESET and is active.
INF: CMD>CM C:\Freescale\CW MCU v11.0\MCU\bin\Plugins\support\s12z\gdi\P&E\freescale_9s12zvca192_1x16x96k_all.s12zp
INF: Initializing.
INF: (Bus Freq = 12487KHz)
INF: Initialized.
INF: ;version 1.03, 6/27/2014, Copyright P&E Microcomputer Systems, www.pemicro.com [freescale_9s12zvc192_pflash]
INF: ;device freescale, 9s12zvca192, 1x16x96k, desc=all
INF: ;begin_cs device=$00100000, length=$00030000, ram=$00001000
INF: Loading programming algorithm ...
INF: Done.
INF: CMD>VC
INF: Verifying object file CRC-16 to device ranges ...
INF: block 00FD0000-00FD015C ...
INF: Calculated CRC-16 does not match block. (File = $F353, Device = $026D)
INF: CMD>EM
INF: Erasing.
INF: Module has been erased.
INF: Reloading programming algorithm ...
INF: done.
INF: CMD>PM
INF: Programming and Verifying.
INF: Processing Object File Data ...
INF: .
INF: Programmed.
INF: CMD>VC
INF: Verifying object file CRC-16 to device ranges ...
INF: block 00FD0000-00FD015C ...
INF: Ok.
INF: block 00FFFFFD-00FFFFFF ...
INF: Ok.
INF: Checksum Verification Successful. (Cumulative CRC-16=$DF72)
INF: CMD>RE
INF: Initializing.
INF: Target has been RESET and is active.
Starting 3rd party flash programming...
GDI: Mtwks Callback(MTWKS_CB_PROJECTACCESS, Section : STARTUP, Entry : SPECIFY_NETWORKCARD_ENABLED, Value : 0, R) => DI_ERR_NONFATAL
INF: Copyright 2012 P&E Microcomputer Systems,Inc.
INF: Command Line :"C:\Freescale\CW MCU v11.0\eclipse\..\MCU\bin\de.exe" -noni -language en -ORBendPoint giop:tcp:127.0.0.1: -ORBtraceLevel 0
GDI: Mtwks Callback(MTWKS_CB_PROJECTACCESS, Section : PEDEBUG, Entry : IS_GDB_CONFIG, Value : 0, R) => DI_ERR_NONFATAL
INF: CMD>RE
INF: Initializing.
INF: Target has been RESET and is active.
INF: CMD>CM C:\Freescale\CW MCU v11.0\MCU\bin\Plugins\support\s12z\gdi\P&E\freescale_9s12zvca192_1x16x96k_all.s12zp
INF: Initializing.
INF: (Bus Freq = 12487KHz)
INF: Initialized.
INF: ;version 1.03, 6/27/2014, Copyright P&E Microcomputer Systems, www.pemicro.com [freescale_9s12zvc192_pflash]
INF: ;device freescale, 9s12zvca192, 1x16x96k, desc=all
INF: ;begin_cs device=$00100000, length=$00030000, ram=$00001000
INF: Loading programming algorithm ...
INF: Done.
INF: CMD>VC
INF: Verifying object file CRC-16 to device ranges ...
INF: block 00FD0000-00FD015C ...