A CF card should always be set to master on the CF interface if the end user wishes to boot from it.
Perhaps the problems you are experiencing stem from using a card that is providing information at too fast a rate or one that isn't fully compatible with the interface. Both have been known to happen, especially with today's CF cards that are marked as 40x and faster.
*Addendum*
You might wish to go back into HDToolbox and see how the card is setup (MaxTransfer and Filesystem) wise as Countzero suggests.
I recall one one occasion, I had to disable the Directory Cache at the CF card formatting stage as this caused no end of problems. Perhaps this is also a mitigating factor in the problems you are experiencing.
