That seem as a partition problem.....
Make sure the bootable partition is in the first 4GB range of the hard drive..
Also that partition must not be greater than 4GB, although I would recommend a boot partition way smaller than 2GB.
3.9 does support partitions greater than 4GB *BUT* until first reboot that the new rom is initialized amiga is only working from 3.1 rom with all known limitations.
Hope that helps....
