Just as an update to this, there might be something about the 32GB CF cards in general and the custom dual-boot bootloader has nothing to do with it. I did try switching the 32GB CF card into the X5 that has the 256 GB CF card and dual-boot. The X5 still throws up the HDD error with the 32GB card when trying to boot into the original firmware. It did not throw up the HDD error with the 256 GB CF card.
Further, I bought a CF/SD card adapter from iFlash and put a 32 GB SD card (full size SD card, not micro SD with an adapter) into that and it boots into the original firmware just fine.
Bottom line, 32 GB CF cards might be trouble or at least the ones that I bought and linked to above.