The MCS boot-loader firmware has config fuse options already set. You cannot over-ride these when loading your code into the target using the boot-loader software.
I.E. whatever the config fuse settings are in the loader firmware you're stuck with.
The only way to change config fuse settings, when using the MCS boot-loader, is to re-program the PIC with a different boot-loader firmware file.
Whatever config fuse settings you may have embedded in your .hex file at compile time are simply ignored when you load your code using the boot-loader software. The boot-loading process does not alter config fuse settings.
Note: The MCS boot-loader works only with an external oscillator. If you change this in the loader firmware before programming, it probably isn't going to work. At least not reliably.
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