Ok, normally I have a system that just has debian etch.  I got a new
harddrive, and decided that the old one would be a good way to make use
of the win98 coaster I had laying around.
Win installs what passes for perfectly, and so I plug back in hda (I'd
cut power to it so windows couldn't "assist" me with the mbr).
Ok, boot up debian, and set GRUB with the map (hd0) (hd1) and vice
versa options.
windows boots.  groovy, except that now I have 2 of every windows
drive, and 2 more drives that I think it imagined, and I also have no
DMA support on any drives... bummer.

reboot linux for an experiment... I get a big warning that I have to
goto maint mode, run fsck on / and then reboot.  no errors, reboot goes
perfectly, all is well.  ~shrug~  weird.

Well, what the hey, win can't read ext3, so I drop the map of hd0 and
just tell grub map (hd1) (hd0) and removed the opposite line.  Windows
boots fine, the duplicate drives are gone, but the mystery drives and
dma issues remain, well, that's not good and it occurs to me that the
other map line might be there for a reason... so reboot to put it back.

big warning that I have goto main mode, run fsck, no errors, reboot all
is swell.

I just to test things drop BOTH maps...  windows fails to boot,
rebooting to linux I again must run fsck and reboot.  I'm noticing a
pattern by now.

My BIOS boot sequence allows me to boot different harddrives first, so
I switch it to the windows drive, GRUB is skipped by of course and
windows boots up directly and with DMA, no imaginary or duplicate drive
~cheering~ goody, now I can run GCA (yes I installed windows to run a
7MB program...  ~shrug~ it doesn't work in wine yet)

Ok, now that I've fixed my character and had to reboot a few times due
to explorer crashes....  I was longing for linux...  reboot, reset the
bios.  NO FSCK...  I go straight to X.

Alright. Now...  why is it that booting windows from grub makes Linux
THINK I have drive errors, and makes Windows think I have drives that I
don't have.  Why does booting from the BIOS NOT do this?

I don't WANT to put the windows drive as primary master and use boot
magic the idea here is that windows exists simply because I have
software that I've not the power to run in wine or that won't wine at
all.  Besides, I'm bugged by the idea that even doing that might not
help since I've no idea why it would be having this problem.

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