You need to give us more details about your system and how you partitioned your CF.
- What Kickstart version do you have?
- What partition size for first bootable partition?
- What filesystem used? What was the DosType value?
- What values have you used for Max Transfer, Mask, Blocksize
Also have you tried giving a reset (Ctrl-Amiga-Amiga) when you opened your system and disk didn't boot?
Did you have an PCMCIA adapter inside the Amiga when you were trying to boot from the internal CF?