I have a dual boot system with win98 and 6.0. I booted your 6.1 disk, after selecting upgrade it said no linux partitions found. Just to check I then selected install and fdisk, which found my linux partitions. Also on rebooting I was able to boot into 6.0. I tried this repeatedly. So your install/upgrade program is broken.
We will need you to post a copy of your current /etc/fstab from your 6.0 installation as well as a copy of what fdisk -l lists. Thanks
Do you have any Win98 extended partitions on your machine? These would appear in fdisk as type "f" . . . there are known problems with these partitions and a fix is being distributed the week of October 18th.
*** This bug has been marked as a duplicate of 5511 ***