I'm using the Product Recovery and Diagnostic CD-Rom to try and do a
complete reinstall on my Aptica 2170 with Windows 98. I've done it
before, but I'm having a strange problem this time. The drive is not
being completely reformatted when I select the full recovery option.

Most of the files are still on the computer after the disk has run and
I am prompted to restart. The desktop is the same, the documents, the
program files are still there, and other files too. None of them are
being erased. The only difference really is that the programs are not
installed (according to Windows Add/Remove Program list) even though
the files are still on the computer and the original programs that came
with the computer are being added back in. I've tried the process
several times and I'm getting the same problem.

Can anyone help?

If you don't need anything on the drive, maybe an FDISK of the drive is
needed to wipe everything off this time.

Yeah, just format C: before doing a recovery.
No need to FDISK.