Has been some time but I think I ran into this too and as far as I remember it's not safe to continue if this message is brought up. Did you use the right parameters?
If nothing else helps reformatting the image with windows' fdisk and format might.

The message is probably triggered if the partition start/end in the MBR and the disk geometry don't match.

The link to this utility seems to be broken. What is the current preferred method for creating DOSBox disk images? I want to try installing FreeDOS to a HDD image.

It's included in my 'Megabuild'.

bochs images usually work fine.