I have booted OSs from an eSATA external HDD. My eSATA connection was a direct cable crossover to backplate, your card may be interfering with the boot.
What system is this on?
If it's a desktop, find a SATA to eSATA backplate cable, they are usually less than $10. With this connection the OS and system has no way of knowing it's not directly connected internally, because it actually is.
Let us know if you get this resolved.