I don't think you're seeing a problem with the minimal MBR code from your internal drive. Rather, I expect your BIOS is executing the MBR code it found on your external drive.
If you power up the computer with both drives plugged in, can you edit your boot device search order in your BIOS so that the internal drive is selected ahead of your external device by your BIOS? Perhaps you can remove the external drive from boot search entirely?
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