The F1 and F2 are different revisions of the device.
The Spc5634MF2MLQ80 is mask set 1M35Y and the Spc5634MF2MLQ80 is mask set 2M35Y.
The differences between these 2 mask sets can be found by comparing the errata lists for the 2 revisions of the MCU.
http://cache.nxp.com/files/microcontrollers/doc/errata/MPC563XM_1M35Y.pdf
http://cache.nxp.com/files/microcontrollers/doc/errata/MPC563XM_2M35Y.pdf
The differences are:
e3159: MPC563xM/SPC563M: MIDR MASKNUM field is set to 0x21
e5909: MPC563xM/SPC563M: MIDR MASKNUM field is set to 0x22
ANd the F1 (1M35Y) also has this additional errata:
e5128: eQADC: Some channels do not meet SNR specification
These changes would not explain why you would be having an issue on the earlier revision devices.
I am not certain what the issue you are actually seeing is. Are you not able to initially program the flash on 10% of the the older revision MCU? Or are you having issues programming the flash from code running on the MCU?
Could it also be that 10% of the devices are not communicating with the programming tool?
From quick look at your schematics, I see that VSTBY (BSTBY in your schematics) has a 10K pull down resistor. This should be a 0 ohm resistor. This may prevent access to the SRAM by the programmer or by code running on the MCU. This could occur on any of the devices, not just 1 revision or the other.