I went through the same mess on my A4000 (also kick 3.1). It detected the disk allright, but the drive started
{bleep}ing up, especially when overwriting files (just appended to the file until the partition was full.)
I have no idea if our problems are related at all, but my solution were as follows: I ripped the drive out of the Amiga, did a partition+format on a PC (WinUAE), re-inserted it and everything has worked like a charm ever since.
If you have a SCSI card in your PC, give it a try. It might just work.