For a floppy disk to be bootable under Kickstart 1.3, it must have a KS1.3 compatible boot block, and if it's a DOS disk, it must be OFS formatted instead of FFS. This is the reason why you are having problems with booting from your 2.04 WB disk. Here the Amiga (under KS1.3) will find the disk to be non-bootable, so it will try to boot from the harddisk instead, which fails since most WB3.1 executables does not work with KS1.3.
Your question raises so many others in me though. For example: Why should it matter what FS the hard drive has if it is supposed to be booting from floppy? Or is the mismatched FS a symptom of a bad floppy drive or something?
- Bo
This is because under KS1.3, the Amiga can boot from harddisks with FFS, but not from FFS formatted floppy disks.