If you are having problems booting without the nexus card and hard drive, you have some other problem in the system.
If you are having problems booting without the nexus card but same hard drive on another hard drive controller, you have a hard drive problem.
Otherwise, you have a nexus card problem.
My hard drive controller has this switch on the card itself for autoboot or not. I guess the hard drive also has to be enabled for boot as well. So both should be taken into account. If you cannot disable autoboot on your card, you may still have a problem booting if your 250Meg HD is an auxiliary and working and not enabled for boot.
On my system, the system will boot eventually boot from floppy if the hard drive is bad but controller is good, but you just have to give it a long wait (all retries time-out).