MSP430F2618: MSP430 Flasher Issue

When I load my firmware hex file onto my controller with FET-Pro430 (Elprotronic) the board runs correctly.

When I load my firmware hex file onto my controller with MSP Flasher the board runs incorrectly. (Possible internal parameters are wrong??)

When I read back the memory files after both are programmed and compare the two files, they are completely the same except for

the file from the  FET-Pro430 upload has two areas of extra data (MSPFlasher data has all FFs):

:10320000302E32006D6661696E766973696F6E315A
   to
:10336000803F0300000059DFFFFFFFFFFFFFFFFF6B

and

:10400000302E32006D6661696E766973696F6E314C         //same data as above
   to
:10416000803F0300000059DFFFFFFFFFFFFFFFFF5D       // "         "      "     "

 I tried erasing memory differently ALL or just MAIN but no difference.

Does anyone have any Ideas how to get MSPFlasher tool to work correctly.

MSP430Flasher -n MSP430F2272A -w rat_3_3_.txt -v -z [VCC] (-i USB) (-e ERASE_ALL)