Have you tried the 'dd' command from a Linux live environment?
Linux 'dd' command should theoretically produce an image that's an 1:1 replication of the original. You may try this if all other methods fail.
I have used 'dd' a few times to clone the finished state of a VM's hard disk, which would then be put into an actual hard disk (or CF card) and it will boot just fine there. So far I haven't encountered a case where the target disk written using 'dd' would not boot.
PS: It's also possible that your CF card is reporting a different geometry than your HDD which may lead to issues. Check the "sectors per track" (or simply "sectors") part of your CF card's geometry. I recall seeing my own CF cards reporting 32 SPT instead of the usual 63, and that caused issues with some bootloaders (like AirBoot), as more sectors in the first track are needed for the boot code. I think those geometry values (namely sectors-per-track part) should carry over if you cloned the disk to the target exactly as it was on the source, as it's technically possible to override the geometry values with your own in the disk's boot records, which can be done using tools like DFSee.