EDIT POINT 1: Damnit, i was just too late , but i wrote all this crap so you can laugh away at it
What is your file system setup ? I am not completely sure how it works having Win98 on D: as i simply have never done that, but i know that it requires some files on the c: drive regardless of its location (note, this is just as win2k also requires). So in reformatting, i beleive you have wiped out some files windows 98 needs to start anway.
I dont know if 98SE can be started from D: if c: is NTFS, i cant tell you as i dont know. If it does however, then IMHO you would be as well rearranging the partitions and resinstall with 98 on FAT32 c: and 2k on D: using whatever file system you like (thats what i do, using NTFS, works nicely).
If however, you are using both FAT32, then i think the best course of action would be to repeat the 9x install, using the same location so as to preserve all data. this will restore any files you inadvertantly deleted and should result in the system booting straight into 98, ignoring 2k. Then i would rerun the win2k install and again use the same location to preserve the setup, but just fix it. This will then allow win2k to fix itself up, and as win98 is already installed, add it to the boot menu.
i have just tried something, and got a new boot.ini if i were to set up 98 as the default:
[boot loader]
timeout=10
default=C:\
[operating systems]
C:\="Microsoft Windows 98"
multi(0)disk(0)rdisk(0)partition(2)\WINDOWS="Microsoft Windows Whistler Professional" /fastdetect
So i believve what you would want for your setup, with 2k on c: and 98 on d: with 2k being the default would indeed be something like this:
[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(1)\WINNT
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)\WINNT="Microsoft 2000 Professional" /fast detect
D:\="Microsoft Windows 98"
However, please DO NOT use this because i say so, as i am bringing this out of the top of my head. I suggest the dual installation routine i talked about above. Note that you dont have to format, just run the installations. If you are using NTFS for the primarypartition, i dont know tht you can boot win98 at all, someone else will need to step up for that one, its not somethng i have any idea about
Hope ive been of some help, but its 4:15am and im going to sleep. Goodnight, hope it works out, ill come see in the morning.
EDIT POINT 2: ok, so it did
