Hi,
I can only do a check myself and tell you what is says in the A4000 User's Guide........
Your computer system comes with 3.5" high capacity disk drive installed. You can use either high-density or standard double-density (880 KB storage capacity) floppy disks in this drive. The Amiga automatically recognizes which type of disk is inserted in the high capacity drive.
Regarding the jumper J351 the A4000 User's Guide says.....
DF1: ENABLE (J351) enable 2nd internal floppy (880K) as DF1: Setting = closed
DF1: ENABLE (J351) no 2nd internal floppy, or 1.76 MB floppy as DF1: Setting = open
I have just checked with both a DD and a HD disk in an A4000 running OS3.9 and the Workbench format tool does indeed automatically adjust to the capacity of 1760K for the HD disk.
This probably won't solve your problem, but may be of some use hopefully
