Sounds like your boot partition crosses the 4GB border. Accessing the area above 4GB is only possible after SetPatch has been run once. So your boot partition has to be entirely inside the first 4GB of the drive. After SetPatch has been run (in your case from the emergency disk) the rest of the HDD is accessible and even bigger partitions work fine.
Edit: You can check your setup with Check4GB from Aminet. Boot without startup-sequence after power-on and run it to check your boot partition.
Bye,
Thomas
